i was having lots of trouble with the brainstem too, so heres what i did:
start off by memorizing the ventricular system. you should be able to draw it, sagitally, from scratch: 4th vent, cerebral aq, 3rd vent, IVF, lateral vent (with all its horns). this gives you a foundation to work with.
now, draw the brainstem around it. medulla only goes up 1/2 the 4th vent, pons the top half of the 4th vent, midbrain on either side of the cerebral aq, and diencephalon (thal + hypothal) at the 3rd ventricle. this should give you a saggital section right down the center of the CNS.
now mark where all your cranial nerves are emerging from. start with V coming outta the middle of the pons for reference, and remember that they emerge according to their number: III above IV above V above VI, etc. that at least gives you a basis for lesion-level detectors, and serves to set up what general regions youre going to find cranial nerve nuclei in the cross sections. ie, you can probably tell your basic cross sections from one another; now use this pic to narrow down the likely nuclei youre bound to find.
that should at least get you started relatively easy, you should be able to get this down in about an hour.
