I take lower branches and inner branches that grow too thick and bushy. That way I can get more light to the buds and I get a better yield overall. The thing is you can remove branches at almost any time during your grow. It's much easier once the plant is in flower to see the small branches that will never develop properly and just clip them off starting at the bottom and working my way up.
The only way to really get comfortable with it is to experiment a bit. It's especially useful to have all the same strain and treat them all differently and see what happens.