Not sure what you mean by "different layers".
Apply the paint in light, misting coats. The build-up will be gradual and will keep from filling in your panel lines.
If you have an indented detail that is supposed to be a different color, use the tape to mask the area off and remove the tape when the painting is finished. For instance, if the windows are only marked by small, indented sqares/circles/whatever shape (instead of being open holes), paint them black, wait for them to dry, cover them with tape masks and then spray the base color. When the base color is dry, remove the masks from the windows and you'll have black windows. Or if the indent is really tiny, this is where the 20/0 fine point is going to come in really handy.
If you're as new to this as I think you may be, I suggest checking out a more model-centric site. It's easier to grasp when you can see hundreds of finished and work-in-progress builds instead of the random kit, here. Here's one of the best modeling sites around - it's like the RPF of model building.
http://cs.finescale.com/fsmcs/forums/6.aspx It's a direct link to their sci-fi sub-forum.
Now here's a bit of advice that I give to every new modeler - go to the hobby shop and buy a few cheap snap-fit kits. If you're going to be painting the Protector, I suggest a few snap-fit planes, as they'll show you how to deal with panel lines. It's better to scrw up on a $10 POS snap-fit than on the model you want to display.
-Fred