Personally, I mix a small bucket of water with enough prime to treat all the water I'm changing. I pour a bit in before I start filling the tank, and slowly add the rest as I'm filling the tank.
Part of the way I do this is because I need to add GH booster, and I pre-dissolve it in the bucket, then add the prime. If I didn't have to mess with the GH booster, I'd just add the prime directly as I filled the tank.
Yes, this does mean some active chlorine ends up in the tank, but it gets neutralized pretty fast by the prime.