Put the parts together without paint and watch where they touch each other. Apply the glue in your mind before you actually take the glue bottle. Large sub-assemblies should be fixed with rubber bands until the glue has dried. This may take up to half an hour. Rubber bands, however, are usually not suited to hold together nacelles and pylons, so you have to do it with your hands.
Clothes pegs are the better choice to fix saucer top and bottom parts.
For masking I recommend an adhesive tape with a smooth paper-like surface, not the flexible ribbed tape that is often used for rough masking on walls to be painted. Look for reference images of starships instead. If not perfectly correct, you can at least make the colors of your model look as similar to the prototype as possible. The studio models of Federation starships are painted in different shades ranging from almost white over very light gray to bluish or greenish gray. Their appearance in the VFX shots, however, is usually different.