I'm not an expert in ship building. It's something I got into only within the last couple of years, but I've finished a few now.
For portholes, I just add a black wash of thinned acrylic craft paint and let it go at that.
My most recent completion was USS New Orleans for the Pearl Harbor Group Build. Here's a photo:
If it's any help, you can follow the progress for building her here:
http://cs.finescale.com/fsm/modeling_subjects/f/29/t/154051.aspx?sort=ASC&pi240=6
Otherwise, there are a number of threads in the ship forum showing builds going on, and they can be pretty useful.
Good luck with your project. And please remember to post photos. We like photos.