If it's a NiCd battery, it's probably best to store when the battery is less than half charged, not on the charger all the time. Using the remote periodically will help keep it in better shape to prevent "channeling" of the cadmium. Even if the pool equipment is off, which it should be at the breaker, turn on the remote and play with it for a little bit periodically. When using it when the pool is open, allow it to get fairly low in charge before recharging and remove from the charger once the battery is full again. NiCd batteries are more prone to "memory" or fatigue if they are used infrequently, charged too frequently or overcharged.
If it is a lithium ion battery, they are virtually free from these memory issues and frequent charging won't cause problems. Shouldn't matter much at what charge they are stored, but I would not store them on the charger either. Probably a decent idea to use the battery a little bit periodically as well, but I don't think channeling is as big of a problem for lithium batteries as it is for cadmium.