Noob question, but I downloaded BootMii as an IOS. Now, I want to get Nintendont, except I need IOS 58. Should I download IOS 58, or wold that overwrite BootMii?
Yes, you should install IOS58, and reinstall HBC after so it makes use of IOS58 by default. Since it's the only official IOS with USB 2.0 support it's the best IOS to use for homebrew. BootMii installs in slot 254 I believe (it's for sure >200) so no worries there.