Honestly, a lot of it comes from sheer observation.
The U.S. Navy Go check their photos. Type in "Super Hornet" or "AMRAAM" or "VFA-103" and see what comes up.
Also, honestly---IMHO, the best source for everything from paint colors to weapons loads to physical differences between variants are NOT books, magazines, or anything official-----but reviews of plastic model kits and the threads where people b*tch about what's wrong with them.
I learned 10x more about what makes an F-15E an *E* from reviews of F-15E model kits (and how they're all wrong) than from reading numerous F-15 books.
Want to learn modern weapons? Go buy a few weapons pack from Hasegawa. See how they show how to mount them, and the rails and racks needed.
That said, feel free to ask me anything. Also, I'd point you to ARC:
ARC Air Discussion Forums Lots of knowledgable people there. I've asked many questions there and learned a lot. Also, any other question has probably already been answered. You'd be amazed how many modelers can stump even a pilot with their questions about "Lot 12 vs Lot 13 Hornet ejection seats", or point out something they never noticed. Modelers pay attention to every square inch of a plane, and look very closely for differences between each subtle variant.
Sorry I can't really give you a link for "modern US Naval weapons and how they're used". I have a few suggestions:
1. Squadron's "In Action" series. Cheap, easy to find in many large hobby shops and online, and good for basic info on the weapons of any particular plane. Not totally accurate, but often very cheap and can form a good basis to start with for the major variants etc. Just about every plane ever exists in that series. Just look for "F-15 in action" "F-14 in action" "SR-71 in action" "T-6 Texan in action".
2. "Detail and Scale". Very few produced over the last few years, many old ones impossible to find. But like better versions of "In Action"----and they've done a wonderful one on the Super Hornet:
Amazon.com: F/A-18E/F Super Hornet: Books (I have the first printing with a different cover--don't know if the new printing has new info or just a different cover)