It depends on the preparation.
I have the Creative Whip which comes with a little recipe book and not all of the recipes demand that you chill after charging. For example the "instant chocolate mousse" is really instant. The only liquid ingredient is the cream itself which is already chilled, and the gas expansion inside the canister chills it even further, so it's ready right away.
On the other hand, if you're making something with gelatin, carrageenan, or any other gelling agent which needs to set, then you'll obviously need to fill the canister while it's still a liquid (otherwise it's going to be rather hard to whip, not to mention hard to get into the canister itself!) and then chill to set it.
Basically it's simply a question of how cold your liquid is before it goes into the canister vs. how cold you want it to be when you serve it. If you can chill it to the correct temperature beforehand, and that won't prevent you from whipping it (as it would with an actual gel), then by all means chill first.
In the specific case when you're using creams and/or cheeses to make a mousse or espuma, you almost never need to chill it in the whipper itself - although it won't hurt either.
By the way, if you're making a gel or anything else that needs to set, it's best to chill it gradually in an ice water bath and shake it frequently as it chills, in order to keep the gas dispersed. If you just charge it and stick it in the fridge, you may find it very hard to dispense afterward.