When I first got my mill/drill I read tales of woe all over the internet about the head going out of alignment when you needed to change tooling. I looked at all kinds of contraptions that people came up with to solve the problem. Then I happen across a video where it was suggested to figure out all of the tooling you would need to use for a particular project and set the head at a height where you didn't need to move the head to change tooling. I have followed that suggestion and so far I have not had to move the head while doing a project. I can't even remember when was the last time I moved the head on my mill/drill. One thing that really helps is using ER32 collets to hold the tooling. ER32 collets are very flexible when it comes to changing tooling.
Back to the issue of tightening the bolts. My mill/drill has 3 bolts. I tighten the middle bolt first then the bottom bolt and finally the top bolt. I do this in stages just like I do when tightening head bolts on an engine.