On some more modern batteries those vent plugs are meant to stay in place, on most it is better to loosen them to let the cells vent while you charge.  If they look like there's no way to pry them out, leave them in.

It's always best to use distilled water if you can.  In some areas the tap water is quite soft and mineral-free, but in others it's quite hard and will tend to coat your battery plates.  It's not the end of the world if you use ordinary water, but distilled is better for battery life.

No need to top them up unless they're getting low, and don't top them right up to the roof of the battery.  There should be minimum and maximum fill lines on the battery casing, and the full line is usually a good quarter inch from the top of the battery to allow room for gas expansion and avoid acid being vented.

The water will run off easily instead of going in the hole, its so darned little. Unless you can pour a very thin, well aimed, sream & then its easy to overfill the cell. I used a syringe, well, I DID, before I blew the poor thing up & replaced it with a Big Crank.