It was to my understanding that 3rd party navbars replace the current one. Meaning if you hide them, then you also hide your 3rd party ones.
Though, if you want to remove them, add this to your build.prop file. "qemu hw mainkeys=1"
You can just scroll to the bottom of the build.prop file and place it there. That's the easiest place for me to remember.
A word of advice. To get back to your home screen, turn your phone off, then swipe right to open Blink Feed. =.P
Remember, you won't have a home button anymore.
As far as customizing, I don't know how. I'm not a themer, or anyone for that matter. =.[
Though, I'm not saying it isn't possible. It may be just too early to ask.
Good luck, and may the odds be eva in your favor.
For the unliving!!