The difference is that PrPro is an NLE, and Encore is an authoring program - different programs for different uses.
To play an FLV you will only need a Flash Player, like Adobe Flash Player, which is free.
...and to make one (flv), use Adobe Media Encoder.
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In a recent, similar thread I confused us by referring to the "flv player" as a "flash player." They are not the same thing. The free flash player plays swf's; an flv player (actually a small swf) plays the flv. You can also embed the flv into a larger flash (swf) program, but most of the time what you are wanting is to play the video in an flv player.
You will see a small swf file in the export to flash you created from Encore; you can upload all those files to your website, but it sometimes requires adjustment for the server address.
You can also use the flash program, import the flv into a flash program, and customize the player skin there.
Putting the threads together helps. I am not sure why the options in Encore for the web and the options from Pre Pro export for the web are so different. I was having a little trouble with the HQ flash file i created from Encore and thought that one of the "Web" options from Pre Pro export might work better.
My conclusion is to use Encore and experiment with the different size/quality options until if find one that works on my friends computer when uploaded to my website.
I have gone through almost all of the "Classroom in a Book" exercises for ID, AI, F,D, AE and Pre Pro (that's alot of $). I am going to try to pick up a reference book for Pre Pro to better understand things like "export".
I have CS3, so I can't comment on the elements of CS4 ame, but I would experiment there rather than Encore. I just don't think the flash encoder in Encoder gives you as much control. You might also want to look at the separate flash encoder (sounds like you have Flash as well I suspect).
But do experiment!
You are right! I am learning this morning that my last post was wrong - I do have more options with Media Encoder. I am now learning how to add the FLV to my website via dreamweaver so that it works.
What a multi-learning curve experience this has been!
The sky's the limit!