I'm actually using WebStorm as the IDE, not the jsreport studio ui. Do I have to do it there?

yes, you have to do it there, using the jsreport studio ui, you should upload the bootstrap.css and bootstrap.js file using the assets upload ui of jsreport studio. whatever you upload with the ui will be moved to the assets directory.

the ui step is needed because we do other things with the asset file (for example we register the asset internally in the jsreport store for future reference), however in the future we are likely to make it more easy to use an asset, just by dropping the file in some folder and automatically recognizing it, but for now you need to register the asset with jsreport studio.