You won't lose anything, it will just boot at startup if you have an sd card with the bootmii folder with the necessary files still on the sd card, you can also change the config.ini in that folder to make it autoboot to either the system menu or the homebrew channel after however many seconds you want.
Just do a boot2 install, use a GC controller to navigate it (or power button to go right and reset button to select from the console itself.) Use it to make a nand backup on a card that has at least like 540 MBish free space on it. Then if you don't want it to load all the time either just rename the bootmii folder on the card to something else or edit the config.ini to say AUTOBOOT=SYSMENU with no # sign in front of it and BOOTDELAY=0 to directly boot or like 2 or something to have it boot after 2 seconds of no other input. You could also change SYSMENNU to HBC if you want it to autoboot to the hbc.
Edit: No it won't erase whats on your card. Only thing that will is if you're using the beta 1 version and do a nand backup. beta 2 which should be the only one posted there now anyways will just write the nand.bin over any existing nand.bin on the card without formatting or deleting anything on the card