I'm still learning too, but I can tell you what has been helpful for me to understand the jackcontrol utility.
Open up jack control. Now press the "connect" button. This brings up a connection window that shows your soundcard inputs/outputs as well as inputs and outputs of audio applications. At this point the connections list is empty... so lets start the jack server by pressing the start button
You will now see that the connections window shows your soundcard on both the output ports and input ports (on mine it is labeled as "alsa_pcm")
Ok, now open Hydrogen, then file->Open Demo Open any demo you want
Also notice that on your connection list Hydrogen appeared on your output ports, and most likely it is already connected to your alsa pcm input ports.
If you press play on hydrogens transport (or the jack control transport) the drumloop starts playing.
Then to make it even more fun, now open up Jack Rack. Again you will notice that it shows up in the connections list. So lets add an effect in jack rack. Click on add, then Time->Delays->TAP stereo echo, then when the parameters for the plugin come up, click on enable
Of course nothing happened yet because we have to route the output from hydrogen to the input of Jack Rack, then the output of JackRack to the input of the soundcard in the connections list. To do this, click on Hydrogen in the Output Ports, and the alsa_pcm on the input ports so that they are both highlighted. Then click the disconnect button. Now highlight the Hydrogen Output Port and the Jack Rack input port, and hit the connect button, then do the same from the Jack Rack output port to the alsa_pcm input port.
You should have sound again, this time being processed by the plugin. Play with the parameters to see the difference in sound!
Sorry if this is oversimplified or if you already understand routing in Jack, but small practices like this have helped me understand how jack operates.
Now I just have to figure out how to use some of the other software and start recording!