Newbie: how not to hit the vice? 2nd op centering?

I have a few ways to figure this out but curious what the real machinist do

What’s the machinist way to determine how deep you can cut without hitting the vise?

2nd op question. So say I want to cut many pieces of aluminum that are cut on a bandsaw. Op1 is done on all pieces and used a mill stop. If I flip all the parts one at a time to machine a pocket on the back side how does everything stay centered assuming the saw cut stock isn’t perfectly straight and isn’t perfectly cut to size? Hope that makes sense

cut stock then square stock while taking to size. Once your on to OPT 2 making a pocket or what ever the cut may be. the depth is figure by measuring from top of part to top of jaws. If your making a contour or outside cut that will tell you how far down your tool or tools making that feature can go depth wise. Real easy to check and double check when setting up, and programming. Once you get thtat down you can setup and run long programs through the night keeping that spindle turning and earning.

Best way to square the stock in the vise without hitting the parallels?
To measure top of stock to the vise use the (not sure what it's called) the small piece that comes out the back of caliper?