This is the source of your difficulty. My approach to gluing up panels is "keep 'em big and thick as long as you can".
Obviously this doesn't apply to your situation, just thought I'd mention it.
That said, there are various alignment aids that will help such as biscuits, dowels, Dominos.
If you don't have the tools for that, a slot cut with a router to accept a spline will work quite well.
Another way is a tongue and groove joint.