Ok, in the end it was pretty easy, however, finding that out, was not.
In core.clj there is this code:
(http-kit/run-server
(if (dev? args) (reload/wrap-reload app) app)
Simply change it to this one:
(http-kit/run-server
(if (dev? args) (reload/wrap-reload app
{:dirs ["src" "checkouts/subproject/src"]}) app)
You can add as many folders you want, all will get watched for source changes.