Using a different merge/compare tool with visual studio is a fairly straight forward thing to do but if you’re using something like winmerge but beyond compare has a lot more bells and whistles to fiddle with. Below is my preferred setup.
How To:
Under Tools > Options > Source Control > Visual Studio Team Foundation Server
Select Configure User Tools. Add both Compare and Merge operations.
Beyond Compare
Compare:Tool: C:\Program Files (x86)\Beyond Compare 3\BCompare.exe
Arguments: %1 %2 /title1=%6 /title2=%7 /solo
Merge:
Tool: C:\Program Files (x86)\Beyond Compare 3\BCompare.exe
Arguments: %1 %2 %3 %4 /title1=%6 /title2=%7 /title3=%8 /title4=%9 /solo
Further Reading: List of other merge tools you can use