Watering will depend on the circumstances and if the bottle is open or closed. It is hard to say how much water.............you don't want the soil soggy. If there is adequate moisture you will probably get some condensation on the side. If the soil begins to dry out you will see it. Flowering plants sound great and would look good at the moment but remember as those flowers die they will have to be removed (long tweezers) or otherwise get brown and probably moldy too. a bit of high maintenance. Otherwise miniature african violets and some other gesneriads may work well. A small orchid may too if soil conditions are right. I have done a similar terrarium using "Earth Stars" (Cryptanthus). They have colorful foliage, grow very slowly (this is a good thing in a bottle garden) and look colorful and nice for a LONG time with almost no maintenance.

If you propagate little wax begonia plants from tip cuttings, they bloom nicely in terrariums (although YES, they do drop a lot of little flowers that you have to take out). I like to root them in a glass of water, grow them on in a flowerpot for a couple weeks, then use them to build a terrarium.