Since the region that the two images cover are very different, centering will provide very bad results, so I would recommend skipping this step.
Yes, you can do the initial alignment fully manually. Instead of the sliders, you may find interactive transform widgets much more convenient to use.
For even better and faster results, you can use Fiducial Registration Wizard module (in SlicerIGT extension). You can place 3 corresponding landmarks on volume-rendered images in 1-2 minutes, which should give you a registration with less than 5mm error.
Before this, crop both images to approximately the common region.
Instead of BRAINS, I would recommend to try Elastix or ANTs, which are typically much more robust (you get good results without having to tune any parameters).
I’m not sure what your end goal is. Just cropping an image does not sound very useful. If you want to stitch the volumes then you can use the Stitch Volumes module (in Sandbox extension).