Although you can't install custom themes on DotNest (see "Limitations") you still have a lot of control over theming. Using Media Theme you can develop themes using Liquid templates and static assets as usual, from your favorite IDE, working with a local version of your DotNest site and deploying code to it. Here's a quick demo of how all this works. Please follow the guidelines of the DotNest Core SDK, and if you prefer tutorial videos instead, check out our playlist.
Alternatively, you can simply use the Templates module for overriding shapes with Liquid.
In either case, the theming work you do will be compatible with any hosting model of Orchard, so if you decide to move your site away from DotNest, it'll still work.