I third the overflow for taking care of the skim. All it will basically do is push that dirtier water at the surface into your filters in the back. On bigger tanks, that water would go to a skimmer to get pulled out of the water. You filter might get some of the skim out, but the overflow will at least make sure that the proteins at the surface are being mixed into the water where they can be dealt with by your live rock, water changes, etc. And it keeps that ugliness off of your water.
Don't know about the bubbles... are you getting any bubbles shooting from a pump (maybe sucking air every once in a while).
On the filter, I honestly don't even use one on my nano. I found that the foam blocks that fit in the back (on the nanos with back compartments) would just build-up junk and I wasn't great at changing them.
Please pardon if this is insultingly basic (and definitely read up more on this):
As far as the filter building up stuff that is good for the tank... that is very true in freshwater tanks where you don't usually use porous rocks like what you do in a SW tank. One of the main reasons your rocks are called "live rock" is because they should be populated with bacteria that should be providing the main biological filtration. So, you would primarily use a filter for mechanical filtration. In FW, fish poo and food getting trapped in the tank is slightly less of a problem because the end result is higher nitrates. Nitrates are not as much of a concern in FW because fish can tolerate pretty high nitrates without major problems.
Corals on the other hand cannot handle nitrates very well (not to mention algae will grow because we use more light). Also, corals can often catch and feed off of a reasonable amount of the extra food not eaten by your fish so they may benefit from a certain amount of suspended food particles (corals are animals and will grow better if fed... as long as you don't get too many nutrients in the tank by doing so). In any case, because nitrates are bad for reef tanks, a primary concern in SW tanks is to reduce the number of places where food gets trapped and breaks down without being processed. Good flow, your clean-up crew, and frequent changing of any filters in the system will help with this... and water changes on a nano will usually take care of the rest (big water changes on bigger tanks are not as easy and therefore more equipment is required...skimmers being the most widely used in combination with a huge number of others).
