We don't have any programming tutorials here for FFmpeg though I am sure there are some on the web.

All of those modules play some part in the ability to convert and stream the video.

Typically a script like PHPmotion has all the required components to "talk" to these modules. Essentially, you upload an mpeg through the script, and then on the server-side, the server will perform the necessary conversions to turn the mpeg into .flv and the script will also then embed the video on a page or pages of the script.

I would assume that you can examine the source code of the script and take only the parts you need, for example, the uploader and then the parts of the code responsible for displaying the video.

You would probably need to ask the script vendor how flexible the software is and if it is open source so that they can offer suggestions on how to modify it for your particular needs. Some vendors may even offer to code your site for you if you ask them nicely and the price is right.

PHPMotion may be overkill for your needs but outside of that you would be writing the php code by hand.