Its relatively simple, although the process is different for LMDE than for LM 10. For LMDE, turn on the ipod first (this is important). Plug in the usb, and when the ipod icon shows up on the desktop, open gtkpod. The name of of your ipod should be displayed in the left hand box. To transfer files from gpodder, click on your ipod, click on add files (for example from /home/whatever_your_ home_is_called/gpodder-downloads). There is a sync feature, but I don't use it. If gtkpod doesn't recognize your ipod, go to edit>repository/ipod options and click on add new repository/ipod and enter the information about your ipod, then plug in the ipod (turned on of course).
In LM 10, a screen will pop up after you plug in the ipod asking what program you want to use for the ipod. Gtkpod isn't listed, so I chose the command option at the bottom and write "gtkpod" in the space provided and gtkpod opens all configured.