Generally speaking audio recorders generate better audio than video cameras, although sometimes in indie production the director or picture editor request that audio is recorded in the camera to skip the syncing process, in that case, use a portable mixer, don't go straight to the camera.
You can also use a mixer to feed both a portable audio recorder as well as the camera for safety purposes.
All shots have to be slated of course, if so is not possible a tail slate at the end of the take MUST be recorded before the picture and audio cuts.
As far as the picture editing software, the work flow for me has been exactly the same, wether the picture was cut in Avid, Final cut, or premiere; You get the picture and the omf or aaf from the picture editor. Remember to ask the picture editor to export the omf or aaf with "infinite" handles so that you have access to the whole takes, not just the bits that the picture editor used. Also make sure to setup your frame rate to the picture frame rate in the session menu (apple+2- on the numeric pad)
Not sure if i've answered the question...