I don't think JDownloads needs any specific integration to work with CB. CB still uses normal Joomla ACL so protecting downloads with different usergroups/viewaccesslevels should work fine.
We do provide our own download manager of sorts, but its primary purpose is for bundling Joomla install packages. It can be used for other things though. It's file based so you basically create a package then just dump your files into the packages folder (wherever you like, but usually best if it's behind public www).
www.joomlapolis.com/addons/cb-package-builder
It's what we use for our own downloads page below.
www.joomlapolis.com/downloads
It also powers our Install from Web.