If the sheet you are in-ining is dependent on the main bootstrap files then wouldn't in-lining it give you no benefit as the elements can't display properly until the other dependecies have loaded?
As I understood it you would want all the styles for the elements above the fold to be inline so that this section displays quickly. It won't have any benefit if the rules are dependent on other css files that are not loaded yet.
I'm not sure this type of optimisation is worthwhile for small sites that are not 'speed critical' as it just makes things more awkward. In most cases just getting rid of 1 or 2 images can give you better results than hours of fiddling with the code.