Without provide any details it is hard to understand who provide what and where they have set ids and classes?
If you talk about Bootstrap than it is just a css framework and not HTML. It provides css rule to use into your HTML. So to use their framework you must have to apply that class / id to your appropriate HTML element / entity. Without that if you would add just css into theme css it is not going to make any difference to your theme.
If you mean something different than what I understood than please provide detail information about your query