That's the problem with throwing in leaf hops, they will float the entire time. I now tie them closed in a muslin sack and weigh it down. Per majorvices, pellets are much easier to deal with when dry hopping. They also soak in less water.
You'll still get your flavor though, just wait it out. And punching them down is fine.
How long did you let it ferment until you tossed them in?
I added the dry hops after 8 days. (FWIW - 1.067 OG, US-05, held at 64F. Brought it up to 67F when I added the dry hops).
While I haven't done a side-by-side comparison, my feeling is that some of the essential oils could be lost during pellet production since they have such a low flash point. Since this is what I'm trying to get out of my dry hops, I'm hoping whole cones will get me more hop aromatics. I'm not sure whether the difference is noticeable, but it makes me feel better so I'm going with it.
When next year's hop crop is released I'll do a split batch of an APA - half dry-hopped with pellets and half with whole cones to to do a comparison.