Well, first off the skimmer. Most people that I know of, and I think Nissan does this too, take out the skimmer. I have placed in it's place, Chemi-Pure and activated carbon. With a small tank, I believe you don't need a skimmer to have a functional nano reef. Now would it help? Probably, but I had no room to put the Chemi-Pure, so the skimmer went. If you don't feed heavy, and keep up on your water changes, you can pull it out.
With the live rock issue, unless you are using PRECURED live rock, then anything you add into your tank will have to be cycled. Best thing to do it just watch your test results, and when all your spikes have gone to zero, you can then add stuff....SLOWLY. Again, if you use precured, then you can start sooner.
Lastly, you CAN remove the bio balls for replacement with live rock. I don't recomend it, because then you also get debris settleing in and around that live rock. I prefer the method of getting enough live rock in the main tank (gives good places for corals) and then putting another filter in the bio balls place.
Hope that helps