I actually know exactly what you're talking about and here's what I do:

- Put Bootstrap in a folder and import it as a framework in CodeKit. (Just like you.)

- In my project folder, I create a LESS file for the project (e.g. project.less).

- At the very top of my project.less I add an import for bootstrap (@import "bootstrap.less")

- I define and customize all my LESS variables within the project.less without touching bootstrap.less.

Yes, this does mean that the variables are being define again. However, this won't matter because what you define in your project.less will override everything else.