It is better to apply the clear coat to the entire model so that the sheen, whether it be flat, semi-gloss, or gloss, will be uniform throughout (will not look uneven or blotchy). Unless you're replicating dissimilar panels, covering every nook and cranny with the desired coat is the norm.
For your second question, as you may know by now, there are three more or less distinct kinds of clear coats: flat, semi-gloss (aka satin), and gloss. As you said, what type you will apply depends on the model you'll be finishing. So, you don't have to worry about glossing unless it is really a gloss coat that you'll be applying and that this is the effect that you're after.