No matter if you topped or not, they will still stretch during flowering. The amount at which they will stretch will depend on the strain along with a few other variables.
You should figure out how much room you have for plant growth first.
Say you have 2 feet for plant growth (this is not including room for your lights). Then you will want to flower at about 7 to 8 inches. You can achieve this by topping your babies again, but down to the height that you want. Then, wait a week for them to stabilize and throw them into flower.
This is only an example, so don't follow it to a "T."
I would definitely look into some stronger lights, like I said before. The more light you have, the bigger and denser your buds will be. HIDs are the way to go, but CFLs will work fine.