Funny, when I asked Elgato this...Currently there is no feature to automatically export recordings to iTunes.
Well, they don't actually have a universal automatic export setting...once you schedule shows to be recorded you still have to go into that scheduled recording list and tick off which shows (or all shows) you want "automatically" exported after recording and then those will be added to iTunes, but you only have to do that once every week or two, then whatever is scheduled will be exported and added to iTunes.
I don't know if EyeTV has been updated yet for the aTV3 and iPad3, with 3.5.4 I believe the highest quality iPad/aTV setting that can automatically be added to iTunes by checking the "open iTunes when done" box is what they call "Apple TV HD," which is 1280 x 720 H.264 at 30 FPS, and since EyeTV still can't deal with AC-3 properly, it's stereo audio. (I do most of my transcodes in Handbrake where you have much more control.)
Export saves a copy to whatever drive or volume you designate AND imports a copy to iTunes. I keep "Copy files to iTunes media folder" checked so I can't tell you what happens when you don't. And to my knowledge, there's no easy way to delete that redundant copy other than manually.
They've had a "prepare all new recordings for iPhone/iPad" setting under "iPhone/iPad access options" for a while, which also creates an H.264 copy...but this
function is different from the Export
function: it does not add the resulting H.264 conversion to iTunes. In El Gato's poorly designed ecosystem the "Prepare" function just keeps that copy in your EyeTV archive, hidden, so when you're using the EyeTV app on an iPad it can stream the H.264 version to you. It was too complicated for them to add live conversion of EyeTV recordings, which an app like Air Video has already been handling well for years, and which would have rendered any need to "prepare" recordings in advance of streaming moot.
That said, you can still add any of those recordings "prepared" for iPad access to iTunes manually, Control-Click on the episode in your Archive > show package contents > then drag and drop the iPad.m4v to Tunes and it'll show up on your aTV via iTunes home sharing.
But you're after the least manual option, so go the Export of scheduled recordings route if you want everything "in" iTunes. I've learned over time that it's best to let iTunes copy all files to my iTunes Media folder and to keep that folder organized because home sharing with Macs and iOS devices works much better that way--I can't vouch for how seamless everything will be for you if you uncheck those two settings, go the symlink route and let iTunes media reside in a bunch of different places.
I may not be the best to advise you, I only keep a small portion of my total media collection "in" iTunes...frankly I don't waste too much time converting EyeTV recordings "for" iTunes, we watch most EyeTV content in XBMC with a Mac Mini. If we want to watch EyeTV recordings on our stock aTV3, we just use an iPad as a remote control, let Air Video do the live conversion and then "AirPlay" it to the aTV3. We also have an older aTV running XBMC in a bedroom and that can, of course, play those EyeTV recordings directly.