Here's a page that probably tells you more than you want to know. It was the first result on a Google search for encode video iPhone
In the future, you might wanna try Google first. (Or you can try the custom google search)
The iPhone uses MPEG-4 or H.264 video. Is it hard to encode for that? Not really, but you don't want to use AE for it.
Dave LaRonde from CreativeCOW.net explains why:
Don't use AE to compress files for final delivery. The various compressors are there only to make quick 'n dirty files showing a project's progress to producers, clients, the kids, etc. AE is incapable of doing multipass encoding, a crucial feature that greatly improves the image quality of H.264 and MPEG-type files in particular.
Render a high-quality file from AE, and use a different application to do the compression. Popular ones are Adobe Media Encoder, Sorenson Squeeze and Apple's Compressor, which comes bundled with Final Cut Suite. Even compressing in Quicktime Pro is better than compressing in AE.
Making good-looking compressed files is almost as much an art as it is a science.
CreativeCOW.net even has a whole forum dedicated to compression techniques.
thanks Szalam, I'll check that page out. there is no such thing as too much information to me, it is all useful.
I think I asked the question wrong before, and maybe this is the wrong place to ask. It's a flash file that links to a movie and I'm wondering if that can be set up to work on an iPhone.