Greg Nelson, who has had the thankless job of running MSN for Microsoft, has left that position and been given the even more thankless task of running the integration of the complex search and online advertising partnership struck by the software giant and Yahoo.

Nelson’s counterpart at Yahoo, according to sources, will be Mark Morrissey, who is currently SVP of Products at the Internet giant.

The pair–pictured above, with Morrissey on left, Nelson on right–will have their hands full in what will ultimately be a two-year effort.

BoomTown’s title for the relationship: A Couple of White Geek Guys Sitting Around Arguing!

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While in Washington, D.C., BoomTown can’t just visit the policy wonks from Internet companies, so I paid a visit to Jeff Chester, the executive director of the Center for Digital Democracy, a nonprofit consumer advocacy group that works to promote privacy and protection online.

In other words, a professional–and much needed–thorn in the side of Facebook, Google and these days, MicroHoo.

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Yahoo and Microsoft are poised to finally sign the definitive agreement that will govern the complex and far-reaching search and online advertising partnership they struck in late July, said sources close to the situation.

If all goes well, the various Microsoft and Yahoo execs–who have been ferreted away over the last weeks, busy dotting all the i’s and crossing all the t’s in the massive document–could even turn in the delayed deal homework to their bosses for signature by the end of the week.

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In what should come as a shock to almost no one, the detailed negotiations to complete the Microsoft and Yahoo search and online advertising final agreement are more complicated than its authors anticipated and are taking longer than expected to complete.

Relax, folks–they’ll get done.

But here’s a more important thing that should wrap up sooner than later: Yahoo CEO Carol Bartz’s gibes about former CEO and co-founder Jerry Yang’s tenure.

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As BoomTown promised earlier today, here’s the first of many filings related to the Yahoo-Microsoft online search and advertising deal announced last week.

The 8-K filing was made with the Securities and Exchange Commission.

A couple highlights: No termination fee and a $50 million annual payment to Yahoo by Microsoft for three years, for unspecified “transition and implementation costs” beyond the agreement.

(Personally, I think it’s for extra Advil needed for the headaches engendered organizing this circus.)

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After all the investor hubbub over the oh-no-they-didn’t deal between Yahoo and Microsoft starts to die down a bit, the pair are now embarking on the path that is the only way toward proving the efficacy of them joining together.

That would be getting a variety of state, federal and international regulators to say yes to the wide-ranging online advertising and search arrangement they announced last week so they can start making it work.

According to sources at both companies, a variety of filings will be made this week, including one to the Securities and Exchange Commission that should provide more details of the partnership.

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Meet Satya Nadella, the man in charge of search technology for the just-struck partnership with Yahoo.

How the search business of Microsoft evolves, improves and, most of all, out-innovates–especially in the face of heretofore withering competition from search behemoth Google–is going to be a big factor in the success of the deal with Yahoo.

In fact, Yahoo has essentially put its search technology eggs in Microsoft’s work-in-progress basket, which must make a series of innovative leaps, or else.

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While at Microsoft HQ last week, right after the online advertising and search deal with Yahoo was struck, BoomTown interviewed a passel of Microsoft execs, including Online Audience Business SVP Yusuf Mehdi, who has been a key player in the many–and mostly disastrous–attempts that the software giant has made to form some sort of alliance with Yahoo over the years.

While Wall Street threw raspberries at the Silicon Valley icon for the deal, Microsoft got kudos for grabbing a large piece of share that it could use in its ongoing battle with archrival Google.

In this video interview with me, Mehdi defended it as a “win-win”–what else is he going to say?–for both Yahoo and Microsoft.

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BoomTown is spending the day at Microsoft HQ in Redmond, Wash., interviewing a passel of execs about the Yahoo online advertising and search partnership.

But, while here, I have not been able to resist trotting out this very funny puppet video by 1938 Media of sweat-stained Microsoft CEO Steve Ballmer gone wild, screaming about how he smoked the Yahoo partnership, to every Softie I see.

Because I am that sensitive.

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One of the reasons Wall Street investors have gone sour on Yahoo’s stock since its online advertising and search partnership was struck with Microsoft was a comment that CEO Carol Bartz made at the seventh D: All Things Digital conference in late May.

In an onstage interview with me, I asked Bartz about what it would take to do a deal.

She answered quite emphatically that “if there’s boatloads of money, and there’s the right technology and there’s the right information we’d have, sure.”

Here’s the video of that, as well details about how the deal talks went bad at D7 too.

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Isn’t it ironic that Yahoo once employed–and for a very long time–top search techie Qi Lu and here he was on stage at the Financial Analyst Meeting at Microsoft HQ in Redmond, Wash., after having just scooped up that business for the software giant.

Lu, who is now president of the Online Services division at Microsoft, was not generous with the details, although he did say making the partnership work was his No. 2 priority after Microsoft’s own search business.

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First up at Microsoft’s Financial Analyst Meeting today, as you might imagine, is CEO Steve Ballmer, who is as bouncy and braggy as I have ever seen him, probably because he is fresh from getting his mitts on a long-sought-after prize–the search business of Yahoo.

But, while Wall Street thinks Microsoft made out well in the deal, the opinion about Yahoo’s side of the deal has been not so positive, with its shares down another five percent today already, after plummeting 12 percent yesterday.

Thus, Ballmer to the rescue!

“This is the one that stuns me, that people haven’t figured it out,” said Ballmer. “It’s sort of, like, unbelievable.”

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The fun never stops at Microsoft, it seems.

Well, not fun–more like a long march of khaki-clad Softies.

They will be on display bright and early this morning at the company’s annual Financial Analyst Meeting, a cavalcade of top execs at the tech giant blabbing away.

Big topics? I am interested in the recent billion-dollar revenue miss in earnings and, of course, more details about the Yahoo search deal.

BoomTown will be there covering it in person, natch!

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With upward of two-thirds of the search market, depending on what survey you use, one would not imagine that Google would worry too much about any kind of hookup of Microsoft and Yahoo.

Think again.

Sources at Google said the company is bracing for a more robust rival, which will force the company to compete and innovate more aggressively.

They add that Google will likely try to keep a low profile at first in opposing the deal announced today, positing that regulators have the same opinion about fewer competitors in the market as they did when opposing a similar Google-Yahoo search deal last year.

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BoomTown was so glad we had this time together with Yahoo CEO Carol Bartz and Microsoft CEO Steve Ballmer, just to have a laugh or sing a song about a major search and advertising deal.

I liveblogged the conference call, which I updated as it happened.

Did Ballmer scream and jump up and down? Did Carol say something naughty?

Read on!

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