I use gPodder and set it to delete podcasts from the local folder after it has synced them with the Clip+. That way they’ll never appear back on the device after I’ve listened to them and deleted from there.
That might not be an ideal solution if you want to keep an archive of all of your podcasts. One way around that is to use some other software to regularly conduct a one way synchronisation of your computer’s podcast folder, to a separate archive folder (e.g. Second Copy, SyncToy or various backup applications).