How do you guys tie the host account to the new authentication system? For example if one is using the LiveID authentication system then I know how easy you tie DNN accounts to liveID accounts but how do you go about the host account?

I'd like to hide the DNN possibility completely and only using the custom authetication system I am developing for my client. but if I hide the normal DNN login possibility how do I then log in as host ?

I would have to concur with Mike, leave your host account as-is, and set the account you are using to be a SuperUser.  That will give you access to the host menu, while you still get all the authentication of whatever provider you are using.

That being said, it is definitely NOT something you want to do very often.  SuperUser accounts are not treated like normal accounts, and you will run into problems with a whole bunch of modules that do not play nicely with SuperUser accounts.   Since they have different access levels, permissions will be off, uploads won't work right, settings won't change, etc.  I've run into a heck of a lot of problems with that, so I ended up removing the SuperUser account status on most of my accounts just get thing working correctly.