Thank you all for your replies!
Well, as of right now the volume of work for this kind of distribution seems like it will be limited, so we might just have someone do the encode for us from my uncompressed/lossless sequence to make sure everything is right, but I still want to learn (and understand) how to, and what is going on, and if we end up doing more of this type of delivery, possibly purchase a license for the software you have recommended.
Until now I haven’t had to worry since most of it has been usually just smaller videos that are placed on a website or as part of a presentation, so a LOT of flexibility regarding output files.
Craig, that been said, I still would be interested in that template, as I mentioned, really interested in understanding all of this, so the more I play around and see the various results and see what people are doing, etc, the better I will be down the road.
Thanks once again!
-Alex