There should be two little round stoppers with a hole in the middle. They are the end caps! They are VERY necessary! You put the two end caps on either end of the tube...(the clear plastic or glass cylinder thingy) Then you push the cartomizer down into the tank. The end with the threading is the bottom side, and those threads must be exposed to thread it onto your Provari. The other end of the cartomizer should be flush with the top of the tank. You have to fill the carto first and then the tank.
If you already have a flavor in your carto and then put a different flavor in it, you will be mixing the flavors and it will take quite awhile for the second flavor to come through, if ever, I'm not sure because I've never done this. The normal procedure for changing flavors is either to have a different tank and carto, or empty the tank and get a new cartomizer.