Ok, most of the time i like to play songs that are downtuned to Drop C, Drop B and sometimes Drop A# etc. I know what strings i want for the job, Ernie Ball Not Even Slinky's.
But i was wondering that if i set my guitar up to play these downtuned songs, would i be able to tune back up to Drop D and standard tunings without messin up the truss rod and all that other shit you gotta fiddle around with?

The strings are a custom guage: 12, 16, 24(plain), 32, 44, 56.

12's are pretty heavy for Drop D. But then again, that's probably what you're gonna have to swing for Drop A#.
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You'd have to make truss rod adjustments when you change tunings that drastically which really isn't that great for your neck. You can do it, it's just not advisable and could eventually lead to it warping if you do it too much. If you just leave the truss rod alone when switching tunings you'll wind up with strange neck reliefs. I'd get one guitar for C# to E and one for C and lower.
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You'd have to make truss rod adjustments when you change tunings.

This. It has the potential to screw up your neck if you do it yourself, or too often. So you should do what I used to do before I had a 'baritone' and 'standard tuning' guitars : Use a pitch shifter.
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