Use an allen wrench for the "empty holes", that should most likely work.
And I assume you mean heel up when you said "move my legs up on the pedal". This is a common problem regarding control when you're playing heel up. Look at it as a trade off if you want to, most drummers get less control playing heel up, but better speed and stamina. On the other hand, heel down gives you better control, but for most drummers, they find it very taxing to play heel down. But ultimately, it's just a matter of preference.
So yes, try using heel down when playing constant bass drum notes at slower tempos.