We use little tabs that we make (thin plastic 1"x1" with a piece of acetate glued to the bottom so the paper doesn't slid underneath). If the print needs to go up then you move the tab up the corresponding amount. Three tabs are all you need. One for the right bottom corner and two along the bottom. If you are using deckled paper then cut off the deckles on the two sides you need for registration.
Use registrion marks that are on each color (film positives) and have a few sheets (paper) that are just for this. If you know that all the reigstration marks from color to color a hitting right then it all a matter of pre-registration.
What I normally do is find out exactly on my paper I what my image to print. Then I draw lines so I'm straight as I can be top to bottom and side to side. Example: 1" from edge of print to edge of paper if I'm printing 11"x17", I would draw a 10 "x 16" guide lines on my paper. Then that becomes my point of center and all screens should be shot to that point. I've done the old eye ball that looks right when I first started out only to realize I've maxed my adjustments out and now I have to move my paper and then I would chase registration. That same thing goes for where you are placing the paper on your table top or vacum bed. If you make sure that these things are going to exactly same spot color to color (screens) and sheet to sheet (vacum table or table top)
I know it sounds simple and no big deal, but if you do as much pre-registration so screen to screen and paper to vacum/table top then it should all come together alot easier