You can use the same release repository for multiple ROS distributions, all the tags and branches which are created are prefixed by the ROS distribution.
There's nothing special to do for a new ROS distribution, just make sure to use different track names, so if you did:
$ bloom-release -r indigo -t indigo my_repo
Then you'll want to do this for hydro:
$ bloom-release -r hydro -t hydro my_repo
The only other thing I'd tell you to do is to make sure you version numbers are setup correctly across distributions. It's ok to have the same version number between hydro and indigo as long as they do not diverge. When you fork your source code to do something different in indigo you should also bump your minor number in your version, so that you have room to make new, non-colliding versions in hydro. For example, let's say you have 1.1.2 in both hydro and indigo, but you need to fork and release a new version only for indigo, then you should release it as 1.2.0. This is because if you need to make a new release of hydro in the future you want to continue with the patch, as 1.1.3. This way all hydro releases are 1.1.x and all indigo releases are 1.2+.