If you are going to weather your models, then the weathering medium you use should determine your clear coat. For example: say you weather your models with artists oils, then you should use an acrylic clear coat, such as Future Floor Polish to seal your models that way the solvents in the oils do no attack the clear coat and the paint underneath. Or if you weather with acrylics, try using a solvent-based lacquer, such as Testors Dullcote, Semi-Gloss or Glosscote.
As to the question of dull vs. gloss, I prefer using clear coats with a gloss component to better replicate the appearance of metal. Flat finishes are fine for extremely old heavily weathered models, but ruin the appearance of a locomotive or freight car that's supposed to appear "new."
As with any application of paint, a few light coats are better than one heavy one. And always start off with less than you think you'll need to do the job. It's easier to come back an hour or two later to find that you need to spray some more clear on your model than it is to strip the model bare and start over.