Keeping the ProChannels from overloading can be a frustrating business. You really have to keep your eye on everything at all times.
The hardest one to maintain is the Master ProChannel, because it's affected by the outputs of all of your tracks. At least with a track ProChannel you can pretty much work out what's overloading it instantly by looking at the lights on the modules (although the FX Chain light doesn't appear to work...has anyone else noticed this?)
Sometimes an audio clip or loop will overload a ProChannel right out of the box at the first stage. In these cases, an FX Chain gain slider won't fix things. You have to use the gain pot at the top of the channel. I've seen a few of the Cakewalk content loops overload the PC with all modules turned off.
One thing to remember is that a track's fader won't affect that track's ProChannel gain staging, but the sum effect of all the track faders will affect the master ProChannel. Sometimes it can be really hard to maintain a balance. On the track I'm working on right now, I thought I had a good mix balance with nothing clipping, but there was one note on a synth that kept pushing the master ProChannel into the red. The same note, every time. Turning down that synth a little stopped it happening, but then it was too low in the mix. It's frustrating because the master ProChannel can be clipping while the master channel itself is nowhere near clipping. I tried putting an FX chain in the PC and lowering the gain a little, but that didn't work. The actual signal going into the PC was too hot from the get go. So I had to turn every track down by the same amount. Problem solved.
It's probably not worth worrying about "occasional" red lights too much until you're really ready to finish mixing, because you can spend ages trying to gain stage everything and then you do something else to the arrangement or play with EQ or saturation and then it's clipping again. Most of the time when that red light is going off, I don't actually hear any difference.
The worst culprits for overloading a PC in my opinion, are the tube saturation and saturation knob modules. I usually find myself turning the output of the tube saturation module right down. I'm also finding it necessary to turn the output of synths way down. The Z3TA+2 synth is crazy, I usually have to have the master volume turned down to 20-30% in order to prevent overloading.