I am using Bootstrap Twitter base with local overrides.
I am using the individual LESS implementation of Bootstrap 3 , following this Smashing Magazine article to fit existing styles as well as possible. This makes it easy to upgrade Bootstrap while maintaining your settings. This way I have all the basic font-size and border-radius etc ..
I keep my old style sheet, which still undoes everything to fit the old site as much as possible, to resolve conflicts when I go.
The biggest problem is to make sure the grid is consistent.
Over time, I delete sections of the old style sheet and just leave customized Bootstrap.
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