I don't tend to have a lot of cuts per track. So, I guess I just don't mind the "pain". What I use most often is volume automation. That's what its called in the Sonar that I use. I put the cuts together into a new track, then turn on the automation write in that new track. I turn down volume just before the click, then turn back up after the click. Could be a very short duration volume change. Can't control that manually with sliders, but the automation does it nicely. And, since the automation is already on, I kinda use it to modify volumes on the rest of the track. Bring a weak attack up a bit... take a strong one down a bit. Sorta like a compressor that acts differently note to note.
Fender P #913 - P&W Bassists #1105 - Wash. Bassists #81 - Greenboy Designs #101