Part of the problem is when you were throwing from over the top you got used to the release point, and in fact it is easier to see it out of the corner of your eye when you throw it over the top. Also when thrown from over the top your curve was "pulled/accerated" almost straight down as it rolled over your fingers.
Now your arm is further away from your body, and the natural arm arc pulls accross your body somewhat more. When you threw over the top your arm natually went from above your ear to your hip. Now at 3/4's it is about ear height and wants to travel to your opposite side depending how high or low you 3/4 arm slot is.
Everything is a trade off. When you throw straight over hand you get the pulses and minuses of throwing from that arm slot. Pulses more supposed rise on the fastball, more drop on the curve (12-6), but very little movement on a circle or three fingered change.
Now at 3/4's you now have sinking fastball, a change that moves, and a
(1-7 or 2-8) curve (depending where in the 3/4'd world you are throwing)
I think it all comes doen to what kind of pitcher you are or want to be. If you are naturally a hard throwing power pitcher then maybe over the top is for you. If you hands are large and strong did you consider a splitter or a fork ball as a change up?
If you are more of a command pitcher ala Maddux or Glavine then 3/4's might be for you.
I would tabe the slider unless you are at least a Junior in High School.
Changing arm slots is very difficult, I think it is a talent like having a 95 mph fastball. Not many can successfully do what EL Duque' has pulled off for a very long time.
Truly hope this helps,