Here are the steps I try, when a particular song's tempo changes are too complex (and tedious) to program.
I set Logic's tempo to something close to the starting pace of the song, but since I do not assign any audible click, it doesn't matter because I do not hear anything for a guide. I only do it to keep the length of the measures somewhere close to the beginning audio.
I record the song on a single mono or stereo track as audio (if it's a guitar/vocal performance). The recording is done using my own internal sense of time, no external click, and I vary tempos accordingly where different sections require.
Later I listen to the performance a few times, making sure I nailed the BPM and transitions.
Next I assign a simple click like the Logic klopfgeist to a piano key, and while following the performance on monitors or headphones, on a new track I record a MIDI version of the click track.
This is where I run into trouble - I try to set Logic to "Create tempo track" (sorry I don't have it in front of me some of this is paraphrased) from the MIDI click that I created. I know there are a few options in Logic 8 when you do this. No matter what I try, when I apply the tempo map created from my manual click input, it "stretches" the audio I recorded, especially if it's punched, and the audio is no longer contiguous. And if I remember correctly, sometimes even the tempo track doesn't "take" correctly and I end up with a mess.
Anyone who is good at creating a tempo map this way, I'd like to hear from you!!