I use them 'as-is' most of the time, but I've used the premixes (the total body bonus workout, as well as the pyramid up or down). One thing I found with the pyramid up only is that once I got used to the full pyramid, it was hard to choose the right weight to make the pyramid up challenging, because I was so used to 2 more sets coming that I held back a bit).
Another variation is to use the pyramid where you go up in reps, but stay with the same weight (the one you'd usually use for the 12 reps). I've done that, after reading about some body builder suggesting it in Muscle and Fitness, and it works nicely.
One thing I always do with PLB is put more time between sets. Cathe and crew change their weights as fast as possible, which I don't feel is possible for me to do safely, so I just go at my own pace. That's the only gripe I have about this otherwise excellent workout: to much "rush-rush" to change weights.