Thanks for the reply!
Yeah I've created my custom theme in the adapt_authoring\temp\6126bbe2f9a87d5b005aea93\adapt_framework\src\theme\ folder and it's based on the latest Vanilla theme :)
The main issue I've come across is that I've been updating the colour definitions in less/defaults/_colors.less which works for certain things, but a few of them are also set in the properties.schema file. So when I preview/ rebuild my course from the authoring tool, I'm not seeing the colour changes.
I was hoping that the force rebuild would take into account the project.schema but it doesn't appear too. Only way I can get the project.schema settings to update is by doing a fresh upload of the theme. I was hoping that I could simply upload the theme as a new version by changing the version number in bower.json,