How to mark measures?
If you are only a few ml off, then I'd say you're doing pretty good for a beginner DIY. 

For bolts and edges on boards I have always found combination square a very handy tool to have. (See picture below) 

The X/Y on a wall gets a little trickier. You need a good tape measure, one that's at least 1" wide so it doesn't have a tendency to bend. Get into the practice of measuring from both sides of the wall and from ceiling to floor from your "point". Then measure again. Make sure you use a sharp pencil to mark your cut or drill point.

Like everything else, this takes practice. good luck.