To start - I recommend hold the rod ever so gently.
When the ball is pinned, you should be able to slide the rod (push or pull) in order to direct the ball to its desired position (which is, probably, slightly behind the rod). When the ball is too far behind the rod, but not deep enough to firmly pin, you have two choices: 1) if you really don't want to move the ball laterally (maybe it's set-up for a pull-shot, but it's too deep) you can gently nudge it. 2) You can carefully move it laterally, like a tic-tac, until it is properly positioned.
Like most ball-control issues, the answer really lies in practice. Toss the ball back and forth: 1) from a front-pin to a back-pin, 2) from a back-pin on one man to a back-pin on the next man, 3) from under the rod to a pin-position, then back again.
Frankly, is this is a issue for you, it is well worth your time to spend countless hours working on ball-control. Turn up all the opposing men and work all four rods on your side of the table - passing the ball up and down, and across, try to use every man on each rod. This is a simple, yet rewarding practice - especially for singles play. It helps: with the pick-up of loose balls, passing from 2-bar to either the 5-bar or 3-bar, etc.
Another good ball control practice is to pass, non-stop, between the 5-bar and 3-bar. If, when you start, you have you men nearly straight down, begin to pass and catch with the men tilted away from the ball. Eventually, you will instinctively feel the point where the ball will pin. This is also a great way to work on brushing the ball as you pass it.
Good luck (and practice)
Paul