How can I safely switch from using badavatar and XeUnschackle on the Internal HDD to using them on a USB Stick?

I have badavatar and XeUnshackle installed on the HDD of my Xbox 360 Slim but they are barely working when I turn on the console. I have to turn it on and off like 20 times to maybe get them to work once.

I want to see if with USB stick I can get it to work with a bigger success rate. Do I have to first erase all the files of badvatar and XeUnshackle on the HDD and then start using the USB Stick with both of them or can I just let the files on the HDD untouched and use the USB Stick anyway?