For anybody interested - I have figured out a way to do this.
My workflow includes:
1. EyeTV automatic export to iTunes
2. iTunes smart playlist grabs any new TV Shows or Movies added in the last 24 hours
3. Automator App runs every morning and grabs all of the files listed in the smart playlist and sends them to iFlicks
4. iFlicks is set up in "iTunes Compatible", "Current Location", "Add to iTunes Off", and "Automatic Delete Off".
This will automatically update the album art, along with other nice metadata that wasn't necessarily captured by EyeTV when it was recorded.
iFlicks allows you to set unique rules to be used on any file during import, and I've had to do this several times for certain TV Shows in order to grab the correct metadata from thetvdb.com. For example, for episodes of The Office, you have to rename the show as "The Office (US)". You can also specify the exact album art to be used if you are not satisfied with the one iFlicks select. All of these rules are automatic as well, so it's truly a hands-off system.
But so far it works quite well. I'm happy with the solution.