That's normal when you first start using it. After you've used it for a while, it won't matter which way you do it. Trust me, I've used it for over 50k miles and I've tried every combo possible.
It has a lot to do with the residual lubricant in the cylinders. You haven't used it long enough for it to smooth things out so that it won't matter how you add it. I stopped adding it before filling when I had all the pumps fail on me at a gas station due to a computer glitch when only halfway through adding fuel. The car wasn't happy about running on double aces for the few miles until I got to another station.