I would be surprised if you get much result from your skimming at this early stage in your tank anyway. One of the things to remember about puffers is that they have no scales so they are very susceptible to ick and parasite issues. I have battled ick with mine twice. Both times he came through it fine, but I would say have a sick tank, and take one that has been at the LFS
for a while. Ask them to feed it for you while you are there to make sure it is eating. Finally about wastes just don't overfeed... When I feed mine I do it one at a time and pick up the scraps that he spits out (which they almost always do). IMO
I would say you should be fine for sure for a few weeks as long as your tank is cycled and parameters are ok.
Hope that helps