My suggestion is just stop using anything but Emacs, when you come across a problem see if you can solve it in Emacs, and then fall back (if you don't have the time or it just won't work). As for work flow, it is pretty much the same as you would normally work. i.e. for a normal ide session you would open/edit a file as normal, then commit (in C-x v v) just as normal.
