Black Spot disease on molly, help!

Question
I just set up a new 5.5 gallon tank for my 6 yr. old.  It was running for 28 hours before I put in two fish: a balloon molly and a guppy. The guppy is doing great, but the molly will spend a great deal of time down nustled into the gravel.  Occasionally she will swim around like a healthy fish, but then ultimately return to the gravel.  I started to realize that maybe the black spots (just a few above the head and on the tail fin) were not pigmentation, but perhaps black spot disease.  They do look slightly raised and they are pinpoint shaped.  This morning, I noticed that there are a few more black pinpoint dots on the body of the fish. We haven't yet seen the molly eat, though the guppy has.  I have a picture of the molly, though I don't see a place to post it on this site.

1.Is this black spot disease?

2. If so, is our tank now contaminated?

3. How do I go about treatment? The store (PetSmart) said they would take the fish back (though they are closed today (Christmas day), but is my tank now contaminated?

4. Should I worry about the guppy carrying it if I should move him to a separate/new tank?  Also, should I assume that all the fish at this petstore are contaminated with this parasite since all the tanks share a common filter?

5. Is there a medicine that I can put into the tank?  I read a bit about formaldehyde baths which sounds a little scary to me, especially since the tank is in my 6yr old's bedroom.

Help!!!  

Thanks in advance for any advice and direction you can provide!

Answer
Lisa,
Unfortunately, most large pet store chains, PetSmart included, know absolutely nothing about the fish they sell. Had this person known anything, they would have told you the following:

1. The molly is a brackish water fish. This means then need some salt in their water.
2. The guppy is a fresh water fish, no salt.

These two fish should not be in the same tank because their needs are different. They also need to be in a group. The best way is no less than 3 mollies and 3 guppies. When you house them right, the tank will have to be larger.

3. Any tank that will have a filter has to be cycled before you add the fish. This is a 6 week process. Unless you are right on top of everything, there should not be any fish in the tank until the filter has cycled.

I do not think the fish are suffering from black spot disease mainly because they are tropical fish. I am thinking they are suffering from elevated ammonia and what you are seeing are ammonia burns. This happens in the beginning of the cycle process and lasts a couple of weeks. This is why having them in the un-cycled tank is not a good idea. I would do a 30% water change now, remembering to add the water conditioner before adding the water to the tank. Also, I would pick which type of fish you want ie: tropical, freshwater, brackish, or full salt, and stick to those types of fish. Whichever you pick, take the other fish back to the store as soon as you can.