Break-in Period:
Skimmers need a breakin period (as mentioned) to build up the interior slime coat that will help the bubbles to climb the walls of the skimmer and deposit the filth in the collection cup. There is probably more to it than that, but that is the gist of it from what I got out of my research on the subject.
Collection cup above the water line:
I have never heard about the collection cup needing to be a certain height above the water line, but hey I'm no expert. My collection cup is about 6 inches below the tank, 1/2 inch above the water line in the overflow repository tank, and about a foot above the waterline in the sump where it pulls its water from. It pulls the same no matter what I'm doing with the tank, water changes, top-offs, dosing, etc.
Pump below the water line:
So long as the intake pump for the skimmer is below the water line then you should be fine. You don't really need to make a huge effort to keep it exactly 1/4" below. I think this is simply to insure that you don't create whirlpools in the tank and diminish the amount of water making its way into the skimmer. All I can say is keep up with your freshwater top-offs when evaporation occurs.
Fixing evaporation problems in the tank:
The only way that I know of to keep the tank water from dropping due to evaporation is to use a sump. That way the evaporation occurs in the sump and the tank water remains level. You still have to top off the water just as frequently, but at least it is not noticable in the tank.
Fixing the increase in bubbles during water changes:
Not quite sure what is causing this one, I'd have to ponder it for a while until it makes sense to me. My first step in this situation would be to spread out my water changes. Change less water more frequently, and try to place the water in the tank rather than in the sump where it would mix with the skimmer before becomming diluted with the rest of the tank water.
Tommysgirl,
Just give it some more time, everything seems to be going well by your description. The green watery stuff is good, that is the skimmate that is being pulled out of the tank. It is always going to be as viscous as it is now, it will just get a lot greener and grungier looking in time.

It took mine a full year before it started working as it was supposed to.
HTH,
Aaron