I'm assuming that you're okay with launching Beyond Compare from the command line, and that you're on Windows. You can add the following lines to your global .gitconfig
file:
[merge]
tool = bc3
[diff]
tool = bc3
[difftool "bc3"]
cmd = "\"c:/program files (x86)/beyond compare 3/bcomp.exe\" \"$LOCAL\" \"$REMOTE\""
[mergetool "bc3"]
cmd = "\"c:/program files (x86)/beyond compare 3/bcomp.exe\" \"$LOCAL\" \"$REMOTE\" \"$BASE\" \"$MERGED\""
Edit: Adding Mac commands straight from site:
git config --global diff.tool bc3
git config --global merge.tool bc3
git config --global mergetool.bc3.trustExitCode true
Then you can simply start conflict resolution with the following commands:
git mergetool # Starts Beyond Compare for all conflicted files, one at a time.
git mergetool -- <file> # Starts B.C. just for the specified file.