I don't often use alligator patches, most of the time I use the basic pattern and play with the attack and release controls. With these you can go from staccato gating to a rhythmic pulsing. You can use the shift rotary to adjust the timing of the pattern to fit.
I also like using an alligator in parallel. Get a spider audio splitter and split the dry synth into a line mixer or mix track, take one of the splits and route it though and alligator into the mixer or another mix channel. Then you can play with the levels fading the rhythmic effect over the top of the 'dry' effect.