This is all part of the game. You should know how tall you want them to be before you flower. You need to root a clone then once it's rooted out it in the final bucket you plan on using. Don't over water as a young clone doesn't need much. Your plant size is dictated by the size of your space. Rule of thumb is the plant will atleast double in size from the day you switch to flower to the day you crop. I personally use a compact space. So I flower my clones no more than 2 weeks after rooting in the final medium.