I do most of my recording without a click and align the timeline to it after the fact, using Set Measure/Beat At Now. I've posted quite a few times about the process, myself, but recently stumbled on this post that has nice screenshots in it:
http://forum.cakewalk.com/FindPost/1989048 Fit Improvisation is less flexible as it requires a reference track with a note event on every beat, which isn't always easy to produce, depending on the composition, and it can't accommodate timing that changes at smaller note durations, while Set Measure/Beat At Now will let you set as many or as few points needed, and at any fraction of a whole note.
Here's a post withe step-by-step procedure. Works pretty much the same for MIDI or audio:
http://forum.cakewalk.com/FindPost/2922802 I should add that it's best to work with a copy of the project, because the tempo changes of both Fit Improvisation and SM/BAN can be undone at the time, but once you've closed the project and lost the undo list you can't easily reverse the changes if you find something wasn't done right later.