heres how i do it....
no guarantees that its the "best" way, but hey, it works for me... so try it out and see if its a good way for you... if nothing more, at least its a good starting point....
i only use FL to make the beat. once the beat itself is done, i will EXPORT it (from FL) to a .wav file. then i will IMPORT it (to the recording program) and record everything else there... ie vocals.
then once you get all the actual recording done, you can listen to the song as a whole, and see if you like everything about the FL beat...(mix wise) if not, just make a note of what you need to correct/change, then go to FL and make the necessary changes, then do the export/import process over again.. and then in the recording program, replace the old FL beat with the new
hope that helped!
-joe