In the game you build buildings and units. The units take up "supply" which there is a limit on. At the beginning of the game you mostly just building workers (unless you scout your opponent is going for an extremely early attack), who mine resources and construct buildings.

The numbers indicate the supply you should be at when you build the structure.

so a 12 hatch 12 pool 12 gas means you get to 12 workers and then build those 3 buildings in that order as soon as you have the resources for those.

For zerg the workers actually become the building, so I assume you hit 12, build the hatchery, build another worker, build the spawning pool, build another worker, and then build your gas refinery.

Yes as zerg the lost supply is counted, so you can either go 12 hatch 11 pool 10 gas or 12-12-12 if you want to be a little bit more economically greedy at the expense of making it much harder to hold 8rax in ZvT as an example.

As you get later into the game people who play more seriously also use the in-game clock, or timing a building placement relative to how complete a different building is to determine building timing. This helps with subtleties like whether you lost your scouting worker or not (-1 supply), if the early game got really weird because you had to build more units to hold some aggression, etc.