James,
It doesn't matter if you have a permanent set up or not. Once you're polar aligned a goto with the RA and Dec of your target will get your mount to point roughly in the right direction. The "trick" for getting the alignment perfect is using plate solving software. A plate solver can analyse an image and tell you exactly where your telescope was pointing (and the image scale and orientation of the camera.) This can be used to find out where your telescope was pointed last night and it can be used to check you're pointing at exactly the same place tonight.
Here's some info on plate solvers from the SGP documentation:
http://mainsequencesoftware.com/Cont...teSolvers.html
Cheers,
Rick.