In the case of doing this, do you utilize the whole download then make the mentioned changes and load the whole thing or do you just take the bundles from that theme and add the bundles into one of your phone?
Just use the bundles as you don't really need the other stuff in that download. Unless, of course, you do then yeah, it would make sense to utilize the whole download.
If you want, then you can combine several aspects into one theme like signal/wifi, carrier icons, etc. I like to keep all themes as separate as possible so I actually have separate themes for folder backgrounds, signal/wifi, lockscreen and springboard widgets as well as icons. This way you have the freedom to mix and match as opposed to choosing one over the other.