[chriswarren]

What program language are you going to be using?

I'd recommend checking out the available integration libraries (http://zencoder.com/docs/integration-libraries/#libraries) that we and our customers have created to simplify your integration with Zencoder. You can read our docs (http://zencoder.com/docs/) and API reference (http://zencoder.com/docs/api) for more information about the options you can set. Our API Builder (https://app.zencoder.com/api_builder) will also help you get started with seeing how some of the options fit together.

As for S3, we work in Ruby and use RightAWS (http://rubygems.org/gems/right_aws). That would handle the transfer of files from your users to S3. If you're using another language I'd recommend checking online for an S3 library compatible with your language.