"side windows" is a little vague, maybe you mean the navigator on the left? or maybe you mean the browser that overlaps the graphics window? Anyway, check out this stuff:
this comes up as the default on your screen and you've just been clicking past it, don't. Stop and take a good look at it. This is the first time that PTC has actually tried to provide introductory material, including how the interface works, to users. I'd recommend printing out the Quick Reference card and going through some of the tutorials. You CAN teach an old dog new tricks. I'm living proof. Today, for example, I learned how to rotate the + style axis display in a drawing to an X. And I learned how to show the extend line of an explode view as a dot font instead of a dash font. Not big stuff, but proof that we're never done learning with Pro/e ~ none of us.