We ended up without having a problem at all! We used a click through mostly every note. Here's how we did it:

1 We made scratch tracks, recording seperately for each change in tempo.
2 Then we mixed them together to make the songs complete.
3 Then our drummer worked his ass off practicing to the scratch tracks (which contained the click as well).

Therefore, when we got into the studio it was just like he had practiced it and we shot through the songs very quickly. We are doing an album with MANY tempo changes (fastest tempo at 300) with 70+ minutes of material, and he recorded it in ONE day. This is the first time our drummer has used a click track in the studio (besides one song we used as a guniea pig). Thanks for all the help you guys, I learned a lot here and used it to our advantage.

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Though, I should mention a few times our tempos didn't feel right, whether we normally speed up during a specific part, the tempo moves up and down, or whatever the case may be... And our drummer played those parts in free time, usually with us playing along with a live scratch track. I think an important thing for the drummer to remember is that the click track is a GUIDE, but if it doesn't feel right, then it's probably not right. After all, you can't hear the click track on the final mix of the song... Unless you're into that sort of thing.