1) What kind of chemicals are you talking about? Is it chemicals to kill the chlorine from tap water? If so, yes, add it to the bucket, and wait a few minutes before adding it to the tank.
2) There is nothing you can do about them getting pregnant unless you seperate the males and females in seperate tanks. If you want to save the babies, remove the female when it looks pregnant, and put it in a seperate breeder compartment.
3) With the fish you have, I don't think they would eat the live plants, although the Bali Sharks might nip at live plants. You could try a few inexpensive live plants, and bury the roots in your gravel, and see what happens. Live plants require more lighting, app. 10 hours a day.
4) You should have some kind of a Ph kit. With the fish you have, you should keep the Ph around neutral (7.0 to slightly alkaline 7.2). You should test Ph at least once a month, as uneaten food and waste from the fish will slowly drop the Ph to acid levels (6.8-6.6).
5) If the Guppies are not too small for the Bali Sharks to eat, then they would go okay with the Mollies, and they also like the Ph level slightly alkaline. Guppies are also live barers that breed constantly, so you will have pregnant females constantly. If you are going to try Guppies, try one male to every two females.
6) I have six fish tanks, three salt water, three fresh water. Two of the saltwater are reef tanks, mostly live corals and invertibrates.

I know I am a little late, but just keep all of this in mind. The tank looks great.

Tom