Problems using bone tool and armatures

I've read that the bone tool and armatures have their fair share of bugs and am not expecting to find the solution to this problem here but maybe it's worth a shot.

My problem is moving armatures - I can add one with the bone tool just fine, but when I actually move the joints in any way, shape, or form, or even just add more frames to it the art beneath it glitches in one way or another; it'll disappear completely or, more often than not, the 'fill' of the art will disappear and various lines will shoot out of position all over the place! Undoing only returns the art to normal once the armature is undone. I have no idea why it does this and I can't really find anything about it either, whether that be a fix or even just other people experiencing the same problem.

I'm just barely new to Animate CC so maybe I'm doing something wrong - but it will work just as I want it to on some things, then freak out on others. I can't tell what I'm doing right or wrong in either situations.. are there rules to using it, like do all lines need to be closed for example with no gaps, something else? Any help would be appreciated, I really find the armature stuff very helpful but it's such a nuisance when it only works a small portion of the time. Thanks in advance.