Paying cumulative upkeep is always optional. If it’s not paid, the permanent with cumulative upkeep is sacrificed. Partial payments of the total cumulative upkeep cost can’t be made. For example, if a permanent with “cumulative upkeep {1}” has three age counters on it when its cumulative upkeep ability triggers, it gets another age counter and then its controller chooses to either pay {4} or sacrifice the permanent.

If no opponent controls a creature, you can’t pay the upkeep and must sacrifice Sheltering Ancient.

You may choose a different creature to put each counter on, but you can also choose the same creature multiple times. The creatures don’t have to be controlled by the same opponent.

Creatures that can’t be the target of abilities can have +1/+1 counters put on them by Sheltering Ancient’s cumulative upkeep ability because it doesn’t target them. The same is true for creatures with protection from green or protection from any other quality Sheltering Ancient has.