Okay so I unlinked my sysNAND and emuNAND. Installed homebrew from the cia file on my emuNAND. When I loaded it and installed a custom theme it showed up on my emuNAND until I restarted the 3DS. Then it showed up on my sysNAND but I couldn't go into homebrew again and the theme wasn't in emuNAND when I re-loaded. That must mean something is going on with the homebrew usage. Could someone help me out on how to use the two seperate homebrews? Will my emuNAND version affect it as well? 10.7? Do I need to install menuhax on emuNAND?