You may have the wiring wrong. Inverted ior backwards you will . Ive seen diagrams improper to orientation of rails up rails down etc.
Avoid trusting wire position and colors as well as L/R Up/dwn Trace the functions and confirm it is what you have too.
It does sound like all you need is controller to cut off, then deliver power how you need to, "whenever it feels right". You better be sure you are in phase though. If it cancels volts oh well, if you double it.... well the electromagnets get good and hot as is. You can duplicate the controller action with toggles. You could use two remote toggle locations, etc if you wanted.
You can use the 1033. How extensively and how exactlt depends on what other supply you use. Two throttle units have the opposing letter variable voltage from most single throttles. If it is constant voltage, direction the thottle moves is redundant. (you could xhoose the 11 or 15v etc constant taps)
But using different taps on the normally smaller accessory unit is not all you might expect.
Pick one 1033 set of taps and phase them to the main transformer.
Any other use off the 1033 should be 100% isolated because It could lead to an out of phase circuit. Some combos of 3-4 tapsets from 2 transformers can't all phase. Some taps actually bypass the breakers as well. ....fuses never hurt and really belong on accessory outputs anyhow. It really applies to any units.
If you change taps you must be minful you may have changed phase or created a feedback loop possibility ( I think CW (rip) once said he hit a 70v pulsing. Ive had one via pulled wire Id guess was about 6-35v pulsed.
Keep it simple and you'll manage fine until you can hotrod alone better 
