Quick guide to publishing an FLV file to FMS?

Actually Flash makes this pretty easy when you publish video from a camera, for this just hook in the camera onto your netstream, then use publish: YourNetStream.publish(streamName, "record");
For more details just have a look at documentation (primarily "flashmediaserver_cs_asd.pdf", page 102) and there are many samples on the Devcenter http://www.adobe.com/devnet/flashmediaserver/

If you're not publishing from a camera, and your FLV files are already there, there's actually no need to stream these flvs. In that case the best is to create a web application around FMS and provide upload capabilities which allow to upload to a directory where these FLVs can then be streamed from. That's not really FMS specific and depends a bit on the web server technology of your choice.