1. The current dye color. The dot only shows up for gear that can be dyed.
2-4. Spend them. Each class gets its own pool of points to spend. So when you put everything into STR on PGL/MNK, then switch to CNJ/WHM, you'll get a fresh pool of points to put everything into MND. Each class you level is basically a blank slate. The only way they effect each other is the selection of cross-class skills you unlock by leveling other classes. A level 10 GLA is a level 10 GLA, whether it's a brand new character or the last class that isn't 50 on that character.

The only class (for now) where the bonus points are something of an issue is ACN, because it's the base class for both SMN and SCH, which favor INT and MND respectively. Most players either split the points evenly (if they want to play both and don't mind being less effective on both), choose one over the other (if they mostly play one job and only do the other now and then), or respec when they switch (there are items you can get from your GC for 10,000 seals to redo the points on any given class).