Some questions that need to be answered

1) Likely the fish disease ich, which is typically brought on by stress from overcrowding, poor water quality, poor diet, fighting, etc. What fish did you have in the tank?
2) Quarantine sick fish in a separate tank and treat with conventional meds that contain copper. Do NOT use meds on your main tank as these will likely kill invertebrates.
3) Depends. Wait a few more weeks before adding anything new. Buy healthy fish and quarantine them before adding anything new to the tank. Don't overstock & stay on top of water quality and you should be ok.
4) A skimmer is a filtration device that agitates water to force dissolved proteins and lipids to foam out of solution. This biological "gunk" then overflows into a collection cup out of the tank.
5) Depends on what inverts you want to keep. Need more info here.
6) Easy to do accidentally, takes a lot of planning to do deliberately. Pick up the book "Clownfishes" by Joyce Wilkerson as there has been quite a bit written about this topic.

Quarantine is a completely seperate tank (say 20 gallons or something) that you can put fish in that are sick or new to heal their ailments or make sure they don't have any. This is done so that your real tank and other fish won't get infected.

I would get rid of the undergravel filter, there are much better ways to filter your water than that. Have a deep sand bed of 4 or 5 inches, a pound of live rock per gallon of water (maybe even 1 1/2 pounds), and plenty of water circulation (some powerheads). Then you wouldn't need a filter of any kind.

I'm not sure about the breeding clownfish question. Makin' fish babies ain't my thing. I'm sure someone else has thoughts on that question.

I hope that helps.