Are you supposed to get most of the air bubbles out of dough before the second rise?
Whether or not to get the bubbles out is a matter of what type of bread you are making. Something with a tight crumb structure, like a milk bread or bagel will probably have a pretty vigorous punch-down before a second rise, but something like a ciabatta might just have a gentle fold.

Any air bubbles left in your bread for the second rise are only going to get bigger (and eventually collapse). If you want a fine crumb, punch it down and get rid of them. If you want an open crumb, try to keep them