I'm planning to try a battlemage and I found an early stone of enchantment. Should I use it now? Will I lose the enchantment if imbue my staff with another wand later on?
Imbuing and enchantment are totally independent. You can safely imbue a new wand later.
However, you most likely want to add upgrades that will affect it, in which case it's better to hold on to the stone.
But you can safely use upgrade scrolls when you turn them into magical infusion spells. It's expensive, so you might still want to wait a little bit with it.