You can always use Bootstrap for scaffolding (the grid is the coolest thing), and use jQM for interface elements and rest of the stuff. They are two different tools with different goals, just that several bits (or "features") of them overlap.
The 2 just don't play well together. When I Include all the CSS and JS files Bootstrap needs to perform all of it's functions, and then include the jQM CSS and JS file - much of the bootstrap functionality breaks or layouts no longer look acceptable.
I have been searching everywhere for a working example/solution for combining jQM's functionality into a truly responsive layout framework! Any guidance would be appreciated.