So you just have choppy places where the audio comes in and out, right? It's not the actual sound of a click track? Highlight each region where you want to crossfade from one to the next (Apple + F, I think. I'm not in front of Pro Tools right now).
Once you've applied the fades to each region, you can hit F7 to get to your editing tools. Pull the heads and tails of each waveform out until you hear the pops disappear.
If you're really, really, really stuck, send me a message and maybe I can help you with it.
1977 Fender Jazz/Ernie Ball Music Man Sterling/Squier VM Jazz fretless
Can Play Bass And Chew Gum At The Same Time!