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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Here is a video interview BoomTown did with Bob Visse, GM of MSN Product Management today at Microsoft’s offices in San Francisco.

The new MSN homepage debuts tonight with a redesign cutting clutter, adding the ability to access both Facebook and Twitter, a local focus and with Microsoft’s new Bing search service everywhere.

Also, some Microsoft interviews with MSN staff about the changes.

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The edging-ever-closer-to-consummation deal talks with Yahoo about an online advertising and search partnership and the aggressive marketing of its new Bing search service aren’t the only things going on for Microsoft’s online services business.

MSN, Microsoft’s online portal, is also preparing a major redo of what U.S. and, possibly, international consumers will see, as it doubles down on five key content verticals, while cutting back on others.

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According to several sources, more restructuring is about to hit Microsoft’s online division as various departments are moved among and between its top execs, with changes to be announced as early as today.

While BoomTown is still gathering information, it looks like longtime Microsoft exec Yusuf Mehdi, who is now in charge of marketing, online audience business development and product management for MSN and the search properties, will get more added to his portfolio, including overall business development for the online properties.

Mehdi could eventually get purview over programming for MSN too, said several sources.

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Here’s part of an internal memo BoomTown obtained about some small, but interesting, changes at Microsoft’s MSN unit, sent out by the GM of its Global Media Group, Greg Nelson, which is under the leadership of–well, frankly–a confusing panoply of people.

That’s why I have been haranguing Microsoft CEO Steve Ballmer for a little digital clarity, especially around its consumer digital businesses and brands.

Ballmer has been searching for an overall head of that business, and it will fall to the person he ultimately selects as digital head to figure out what to do next.

Until then, let’s rearrange some chairs!

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