Quicktime conversion to Flash video

When I drag my Quicktime movies into Adobe Flash CS3 video encoder, I then click to resize the video and enter the specs.  Then I uncheck 'Maintain Aspect Ratio'.  Then I press start queue.  I have been doing this for years but my memory seems to be having a little slippage.  Does this process only send to my desktop the .flv file or should it also send the .swf file?  The reason I'm asking it I'm only getting the .flv file and when I upload this to my server with the intention of putting the Flash video onto a website it asks for the source file which I'm assuming is the .swf file which Flash Encoder is not generating.
If I have forgotten and I'm only meant to have the .flv file, how do we then get that to appear and play as a Flash video?  I have recently changed technical help and this was always done by former staff member.  We need help.  Thank you for your time.
Sheryl

would changing it to a Quicktime movie be more universal for people to view without having to download a plug-in?
Not sure about the "universality" of QT but believe it is generally found as a "freebie" on most PCs and, of course, on all Macs sold today. Don't use Windows Media since a good player with codec runs about $50 for my Mac but admit to keeping the "Flash" plug-ins installed for all of my browsers. Would have to abide by what David said as my one and only venture into flash conversions produced "less than adequate" quality as far as I was concerned.
As filmtex indicated above, Handbrake would be a suitable solution if you plan to convert the entire DVD (or chapters thereof) without edits directly to either MPEG-4 or H.264 files. Of the two, the MPEG-4 output would likely be more universal for QT since it would not require QT 7 be installed. On the other hand, the H.264 would provide files roughly one third the size of an MPEG-4 file at the same level of quality.
However, if you are planning to edit the material to any degree (i.e., extract highlights, break it into smaller files, enhance audio/video content, etc.), then you might prefer an alternate work flow. For instance, MPEG StreamClip (free) would allow you to load unencrypted or decrypted individual VOBs (or the the entire title) into the application and peform minor edits before ouputting material to any available QT format. Or, if you plan to make major edits in iMovie, FCX, FCP, or other such editor, you can convert the VOBs directly to the appropriate DV format for your particular editor.

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