How do I get my wallpaper I made for my theme boot with the theme itself? Also, I have a secondary wallpaper that I'd like to be able to switch to and from with. How do I set that up?

Single wall auto install on theme switch.
Use the theme.ini like in austerity theme
For choice between two use lswchanger-1.2
and then bang command
!Wallpaper .stretch $Wallpaper$wall.jpg
For other wallpaper modules look on
http://loose-screws.com/modules.php

or you could set it inside the theme.ini