I recommend this thread, if you haven't already seen it:
Tips for keeping your mods organized and avoiding conflictsThere are links to various tutorials about merging packages. I also highly recommend trying out CC Magic, if you've got a lot of package files and use a PC. It's far superior to manually merging and re-merging packages all the time. CC Magic is also highlighted in the thread I linked above.
As far as peeking into your package files goes -- that is not a bad idea, but keep in mind that a package file can be comprised of many different resources, depending on the content that you're looking at. If you look at a simple XML tuning mod, you might have only one XML or ITUN file in the package, or you might have several, depending on what is required to make the mod function properly. Objects will require many different types of resources, such as OBJK, OBJD, XML, RSLT, FTPT, STBL MLOD, MODL, IMG, etc. If you are not acquainted with the various resource types requires for objects, or even mods, then you might have a difficult time telling if anything is "extra" or not.
One other thing, you can use NRaas Dresser to prevent pirate boots from showing up on townies. There's also a mod available at MATY that will make the boots invalid for random.