mannyhern,
One of my general rules for modeling is: Assemble first, then paint. This method becomes very important in cases where you may need to fill and sand any gaps or creases between parts. This happens a LOT with AMT/ERTL's sci-fi kits. I like to glue the pieces together, putty or otherwise fill the seams, sand and smooth, and only then put on some paint. This way you won't ruin your paint job with all the sanding that you know you'll have to do.
I can think of at least two more advantages to painting after gluing:
1. Paint reveals hidden cracks, seams, gaps and crevices that you may not have known were there. A primer coat after construction is useful not only to prepare the kit for the final color but to reveal these otherwise hidden flaws. Once you see them, you can fix them!
2. Glue will NOT stick to paint. If you paint the parts before gluing you run the risk of getting paint on the gluing surfaces. If this happens then you need to scrape and sand all the joints prior to gluing; an extra step which may have been avoided by gluing first.
Of course, these are only suggestions but they work for me and I learned the techniques in FSM!! Hope they help. Let me know when you're ready to talk about masking...
Mark