Mcboot is just a sort of homebrew launcher which runs from a ps2 memory card. As soon as you turn the ps2 on with the card inserted it will highjack the boot process and launch automatically. I'm also assuming you ordered one of these modified cards.
Oh, as far as running backups, there are apps that launch games from usb, kinda hit and miss, and ones that launch disc copies. If your card is setup right you should have these already.
One more edit, there are tutorials here for setting this stuff up. I recommend you check em out.