Although you can't install custom themes on DotNest (see "Limitations") you still have a lot of control over theming. Using Media Theme you have the option to host your theme using Media Library. You can keep your Liquid templates there as well as your assets like images, scripts, and stylesheets. You can have another theme enabled as a base theme, but you also have the option to have your media theme the only active one. Please follow the guide and see the limitation in the project's Readme.
Alternatively, you can use the Templates module for overriding shapes using Liquid.