How do you know when you need to throw a ball that is more smooth or more skid flip vs just moving left/right? Trying to get into more tournaments and building up my ball rotation.

Notice the different ball motion shapes in the diagram.  In general you want to avoid early friction (the white) to avoid the dreaded over under reaction.  Of course this is in general and can vary on sports patterns or extreme short or long patterns.  Also you don't always start with fresh obviously as even shadow bowling can put a decent size hole to start depending not to mention the heads don't always stay intact either depending.

One of the keys to understanding ball motion and lane play is to not only understand the lane side to side but to look at the lanes front to back.  Playing the lanes front to back with give you an idea of if you want something smooth or something skid flip.

I tend to go with smoother equipment on lanes that have really clean back ends that fly.  On lanes where the back ends don't overreact, I use equipment that flips hard.