You can, just somethings cant be changed after they're added. You can change character models and background textures and stuff, it's mostly just the menu overhaul stuff that requires a new install. You should keep an iso of your original installation just encase. I had to run bootleg quite a few times to find settings that really worked for me, and I've had to default to the iso twice. Once to fix an issue with the sound and another to remove an overhaul option I'd tried. If you want a classic FF7 look use the PRP models. For HD I prefer the APZ, Whiteraven, and Kela51 models. Try them all and see what you like. They all look better in the game than in bootleg so don't judge purely on first impressions.
