DocsDo something
Combine and cut
Most things you build are several shapes treated as one. A wall with a doorway in it, a hammer that is a handle and a head, a window frame with three openings. There are two moves for this, and they do different jobs: putting shapes together, and using one shape to remove part of another.
When you need this you have two or more shapes on screen and you want them to behave like a single object, or you want a hole in something.
Putting shapes together
Join Geometry takes any number of shapes and passes them along as one thing. The pieces stay separate underneath, which is what you want almost all of the time: each keeps its own colour, and each stays its own part when you export.
Paint each piece before the Join, never after. A colour applied after a Join repaints everything below it, so five careful colours become one.
Union is the other kind of together. It fuses overlapping shapes into a single sealed skin and deletes the surface trapped inside, which is what you want when the result has to read as one solid object rather than a pile of parts. It costs more and it throws away the separate pieces, so reach for Join first.
Cutting one shape out of another
Difference takes a base and a cutter and removes wherever they overlap. It is the only way to get a real hole. Pushing a surface inward can make a dent, but a dent is still one surface, so it can never become an opening.
Make the cutter deeper than the thing it is cutting, so it passes cleanly through, and put its position on a knob rather than typing coordinates. That way the doorway still lands correctly when the wall changes size.
Cutting several holes at once
You do not need one Difference per hole. Wire every cutter into Cutter, or Join them first and feed them in as a group; either way they are all removed in one pass, and overlapping cutters never double up.
Working from one shape placed several times, rather than three separately built shapes, means changing the window size changes every window.
When it does not work
Difference wants solid, convex shapes on both sides. If a cut behaves strangely, the usual cause is that the base has already been cut or bent, so cut first and reshape afterwards.
If a cut appears to do nothing at all, the cutter is almost certainly not overlapping the base.