I recently stumbled upon the Ubustu Feed when I began learning Ardour. They have a great tutorial on how to sync Hydrogen with Ardour:
This tutorial will show you how to sync up the digital audio workstation, Ardour, and the advanced drum machine, Hydrogen. This will allow you to have a full featured drum machine playing in perfect time with your Ardour session. Or, one hell of a fancy click track.
I ran into one complication on my system though — getting Hydrogen to work with JACK. The output sockets just weren’t showing up when I opened Hydrogen, even though JACK was running and working fine. Thanks to a post by schivmeister in the Hydrogen Forum, I was able to get it working by changing ‘alsa_pcm’ to ‘system’ in the JACK portion of the ~/.hydrogen/hydrogen.conf file so that it reads as follows:
Best. Metronome. Ever.