If you're creating a lot of courses in the authoring tool you may be better creating your theme and uploading it to the authoring tool, where it can be applied directly to the project.

If you start with the vanilla theme from Github you can update the LESS variables there, zip it up and upload it to the authoring tool as a plugin.

You will need to setup your theme name and version numbers in the bower.json file too. Details about plugin development and the bower.json can be found on the Adapt Github wiki.

Nick