Hi Michael,
As far as I'm aware, and someone will correct me if I'm wrong, deleting the soundcard in Device Manager simply removes the driver. When you start up Windows, it's likely that Windows will automatically install a driver for it. Even if it doesn't, the computer still 'sees' the soundcard as present.
By disabling the on-board soundcard in the BIOS settings, you remove it from being 'seen' by the computer. This is what I always do. I've never had much luck getting two soundcards working -- it creates all sorts of audio problems for me -- so I set my system so that it can only see a single soundcard.
Regards,
Noel