Smart take on the relationship from a reader who handles these issues:

The way I see it, Obama has given Gates a free hand to pursue a defense budgeting strategy that Gates has long wanted, but rarely discussed by Senator Obama or Presidential Candidate Obama. Gates has been permitted to do this even though the Administration is getting major heat from Congressional barons on cuts to favored weapons programs.  Also, Obama is giving Gates  a free hand on war strategy, as evidenced by the McKiernan firing.
So, if I were Gates, I would be pretty happy. This Reliable Replacement Warhead thing is the only concession so far, and is it really that big a deal?  We all know the Congress would have zeroed it out anyway.  So Gates doesn’t really lose here.
I do worry Gates's words could come back to haunt the Administration during a Senate debate on the comprehensive test ban treaty.

I think this is right, although had Gates won Obama over on the warhead question, the White House probably could have convinced Congress that this was not some kooky Bushie/neocon scheme and that it deserved funding.

--Michael Crowley