I also spent quite a bit of time looking for a convenient way to copy and paste the commands into the terminal, and in the process learned of a key-combination (Shift-Insert, which I gather is widely known) which allows text to be highlighted, and then pasted into another window by simply clicking on the other window and then pressing Shift-Insert. I put quite a bit of effort into designing these lists to be easy to use, and I've included an excerpt from one of them as an example.
Each list consists of a set-command for each channel and subchannel that I might want to watch (it's necessary to set the channel, and then the subchannel, to tune in a program - use the HDHR's GUI to perform a scan and get all the channel/subchannel information) and a single save command, whose FileName slot must be modified to some unique name to prevent recordings from being overwritten, and to allow the file to be easily identified later. The idea is to minimize the need to alter any commands before copying and pasting them (the only field that requires alteration is the FileName field in the save command), and to make them as easy to find in the list. My system consists of a list commands for each tuner, which are then copied and pasted into terminal-windows. But in the meantime, my system is tolerable.) (I suggested such a program to the HD Homerun Recorder's developer, and perhaps he'll get around to it some day. So, I came up with a method to avoid having to use this sorry excuse for a control panel, and to make it as easy as possible to record two channels simultaneously on the spur of the moment, without having to learn to program in Python and to create a GUI's with GTK+ to create a proper GUI for the HD Homerun. Then use the VLC player to examine the two files just recorded, and you'll find that both are the same. Let the recording processes run for a while, and then close the terminal-windows to stop recording.
(This requires using one terminal for each tuner to avoid having to use background/foreground commands, which would be required to use the same terminal-window to control both recording processes.) For a complete listing of HDHR commands, find hdhomerun_development.pdf on the internet. ts, where N is 0 or 1 in a dual-tuner unit) for each tuner.
The HD Homerun GUI provided by Silicondust is pathetic, as you can discover for yourself by using it to set one tuner to one subchannel within a channel, and the other tuner to another subchannel within the same channel, and then entering a "save" command (hdhomerun_config save /tunerN.