Alright, if you want to totally understand a resource, pick one you really really want to learn above all others. Now explore it and tamper with stuff in there, go crazy and experiment. Look at other resources of the same type from the data files and other plugs (don't make modifications to other people's plugs without permission from the authors).
Once you've learned it, start on related resources. For example, if you learned ships, look at weapons or outfits. If you learned spobs, look at systems. Also, keep in mind many of the less interesting resources are typically similiar. For example, the desc resource is pretty bland, but very very simple, as its just for displaying text (not to say the text contained within is bland...). Whereas the ship resource, the heart of Nova, is one of the most expansive and complicated in the game!
System and spob coordinates aren't too difficult, just tedious without a visual editor with which you can place systems with (much like the one Mission Computer has), as you have to put in some, save your progress, load Nova, check the system/planet's location, close Nova, fix it, rinse, and repeat.
Basically, coordinates are just where it appears on the map. For the hyperspace map, its purely cosmetic, since a system can link to any other system. For planets, it determines where they are in the system. The closer they are to (0,0), the closer to the center they are. Its just like plotting points on a graph in algebra, minus all the evil equations and "solve for 'x'". Just remember negative numbers = up instead of down for the 'y' coordinate. Its really simple, the hard part is just getting them right where you want them.