Techs are normally paid flat rate or salary/hourly. Flat rate is a per book hour rate similar to commission.
Pay yourself? Talk to your accountant. Depends on the type of entity you establish.
Shop software, I use garage partner pro. It's cheap and decent, but I haven't used others.
Insurance... May be a fun one it was difficulty for me to get with no ownership previously. We have general liability, personal property, and garage keepers.
Good luck.