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.
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.