Use MC that is Magic Gate enabled! (Sony MC, should be cheap enough)
Unless your memory card is filled, you should be able to install FMCB without affecting your game saves. My FMCB install took 3.5MB, but that's including independent exploit and other homebrews.
If you are using disk swap, just boot the ulaunch, once you're there, plug in ur USB drive with the FMCB files (just dl the noobie package from sksapp), browse in ulaunch for ur mass storage, (this is where you can copy ur saves from your MC to ur USB drive in case you want to, just browse to MC0, copy the files, and paste to ur USB mass storage), otherwise, to install FMCB, select the FMCB elf.
you'll get the FMCB install menu, formatting your MC will wipe everything there, so don't format. I would pick normal install unless you plan to use it on multiple PS2, and after that, you should get the install successful. from there forth, everytime you turn on your PS2 with that MC in the slot, it should boot to a custom menu instead of the original PS2 menu with just browser and options...
Now to play backups, Note that you NEED to patch your iso with ESR patcher before burning it and trying to run it with ESR (ESR is the program that should be installed with your FMCB install). After you patch your iso and burn, you just put it in like a normal game, and it should take you to a silver background screen with many options, just pick the left most one that says launch DVD or something, and play (you'll see pink and green flashes a couple times after launching, it happens with all ESR patched games)