I have started using the Sass flavor of Twitter Bootstrap and I just came up with a sensible way of structuring my files so I can make my own custom overrides without messing with the core files AND keep all your CSS in one file for faster loading.
In a nutshell I put all the sass files into assets/sass and make a subdirectory called bootstrap for the core files. I then make a sibling directory called theme for my custom scss files.
Go to /bootstrap
and inside this directory is a file called bootstrap.scss
which includes all the core components. Rename this file to theme.scss
and put it in the parent directory like this:

As you can see I already have some custom overriding sass includes files already in the theme directory. These will be tacked on to the bottom of the default bootstrap CSS when it's compiled.
The magic happens when you go into theme.scss
and change the include paths like so. Look toward the bottom of the image for the overrides and toward the top for the custom variables reference.
Note: If you want to edit the variables in bootstrap, it's a good idea to make your own _variables.scss
file in your theme
directory and include it at the top of your theme.scss
file. This way you can override the bootstrap variables which will persist with updates in the future.
Then just include theme.css
in your pages and voila. This is how I have started doing it and haven't run into any bugs yet.
I find this the least complicated of the methods I have seen. And when new updates come down I'll just update the core bootstrap files and keep my edits!