Seconded!
Subler is gets better with every update, and it's been revised heavily since the instructions in the above-linked article were written. It improved its web search pull down to bring in the Apple Content ID and the iTunes poster art (which I prefer because it's usually a "clean" poster without all the studio detail all over it) so you can ignore those steps described in the article.
Here's what I do:
(1) Encode the two version of the movie in HB, making sure to web optimize both versions (it's quicker to do it while coding than later, but Subler has an "Optimize" function that does this too).
(2) Open one in Subler and
search for the metadata. Subler will pull in all the file information, including the iTunes poster art and the Content ID. Edit as you see fit (I usually cut down the movie description and copy the short version into both the long and short description fields - one is used by iTunes and the other by ATV) and save the file.
NOTE: Chapters
If you're adding Chapter data, either by manually typing the text or by importing from a text file, do this at the end of this step (2),
before saving the file. When you copy across the metadata in step (3), it will copy the chapters too.
(3) Open the other version in Subler and select File-Import-Metadata. Locate the tagged version of your movie and double-click it. Subler will copy your edited tags into this version.
(4)
IMPORTANT: Before saving the second version,
go to the Other Settings tab, and adjust the HD tag to be the correct setting for this version (it will have copied the setting from the source version). Save the file.
(5) Here's where things have gone a little awry, thanks to something weird in the latest version of iTunes. You used to be able to drag and drop both files into iTunes at the same time and, because of the matching Content ID, it would "nest" the two version into one entry, giving it an "HD-SD" flag.
Lately though, this hasn't been working, which has something to do with the audio bitrate.
To force iTunes to accept both versions, I do this: Drag and drop the HD version into iTunes. While this is copying, open your iTunes library in Finder and navigate to the new folder for your new movie. Drag the SD version directly into this folder. Once it's copied over, select the SD file and "Open With" iTunes - you can close this file as soon as it opens. Now, iTunes will recognize both files as one movie.
(6) iTunes defaults to feeding the HD version to every authorized device, unless you tell it not to. To manage which of your devices get which version of the movie, go to the respect device manager pages in iTunes (you may need to dock your iDevices to do this), and on the Summary page,
elect the SD preference if that's what you want for that device.