Just keep practicing those landings. Shooting touch and goes one right after another cannot be substituted for. Using reference points, when you land farther out than you want, remember where it lined up and change the approach a bit for the next landing. It will take some trial and error, but when you hit your mark keep doing it. I am assuming you have no problem in just getting the plane on the ground in one piece. If you do, quit worrying about WHERE on the runway you're landing and concentrate on smooth landings you can be confident with. I prefer to use the aircraft itself as the reference point, probably going by it's apparent size, although it's not a concious thing. This will enable you to more easily fly at a strange field, or land from either direction with no problems. However you choose to do it, it just takes practice, practice, practice. I know several pilots who have flown for years and still have trouble landing. In every case it's because if they fly three times on Sunday they only land three times.
As to flaps, if you're having any trouble at all landing forget the flaps for the time being. They can be deployed anytime you wish, but normally are deployed on the base or final. Be sure you're very comfortable landing a standard no flap configuration before you start playing with them, as the landing characteristics can change considerably.