I use a pad brush and clean after every section for a couple reasons.
1. It is so fast to perform and I can keep the brush in my back pocket while I polish. It's literally a 5 second operation. When using MF pads, I'll have the blow gun within reach so I can blow out the pads as well. The whole system moves around the car with me.
2. Frequent pad cleaning will yield a more consistent pad surface which leads to more consistent results.
When deciding how long between pad cleanings, do consider the amount of paint you are removing. When compounding, you may remove a lot of paint and need to clean much more frequently. I've also found certain polishes and compounds are much more gummy than others and require more frequent pad changes.