Throne of Geth

You don't have to choose every permanent or player that has a counter, only the ones you want to add another counter to. Since "any number" includes zero, you don't have to choose any permanents at all, and you don't have to choose any players at all.

If a permanent ever has both +1/+1 counters and -1/-1 counters on it at the same time, they're removed in pairs as a state-based action so that the permanent has only one of those kinds of counters on it.

If a player or permanent has more than one kind of counter on it, and you choose for it to get additional counters, it must get one of each kind of counter it already has. You can't have it get just one kind of counter it already has and not the others.