Where do I put the bootstrap css file?
This had more to do with properly structuring my directory, I just finished reading Remo's amazing book Concrete5 for Beginners, In the book he wrote that you should just have the one file main.css
However every site I build I build using bootstrap which has bootstrap.css as well as bootstrap-responsive.css & main.css
Right now I have been stacking them one on top of the other so they cascade properly, is this the right way to do this or am Is it preferred to put literally everything in main.css using @import to grab the css files like in wordpress?
Its up to you, that how many css is required to make the theme working. And absolutely the bootstrap has its own style, you cannot make all css in one single file. So just go ahead with multiple css. There are thousands of sites which has more than 1 css file.
And, typically, one locates additional stylesheets in a CSS subfolder of the theme root.
Yes, Remo's book is an excellent intro for C5 developers!