It sounds like you’re using a built-in Firewire connection to transfer your footage from camera to the computer.
720×480 is the pixel resolution for NTSC DV video. 720×486 is the pixel resolution for D1 NTSC video.
Encore 1.0 dopesn’t support QT movies but Encore 1.5 does.
If your workflow goes from AE to Encore, then I suggest that you output directly to MPEG-2 from AE and bypass QT’s Animation CODEC. The MPEG-2 file can be directly imported into Encore without another decompression-recompression pass which will inevitably result in a loss of quality.
Most users use QT’s Animation CODEC, with a quality setting of 94% (or thereabouts – with no keyframes) as an intermediate CODEC (file format) because it retains a lot of the source quality while minimizing the filesize to a manageable variable.
In your case, you don’t require an intermediate file as you can go straight to an MPEG-2 file (for Encore) form within AE.
Output for Web is slightly different as Flash MX use the Sorenson Spark CODEC; which isn’t available form within AE. In such a case, you will need an intermediate file format (CODEC) for Flash to import and then to compress for optimization for Web delivery.
The intermediate file format has to be of a high quality; taking into consideration of the pros and cons of quality and file sizes. As mentioned, the Animation CODEC seems to do a good job for such a situation.
Having said that, I suggest that you compare between outputting two versions of a sample movie – (1) QT with Animation CODEC, and with the DV CODEC that you use to transfer footage into your computer.
There is also the unknown here which is how you get your files into AE. DO you go through an editing software or do the transfered footage go into AE from the camera without passing through any other software/processing?
By now, you would have realised that there is no possibility of finding a correct answer unless a workflow process is first described. But I am hopeful that you may have picked up a few pointers.
There are a lot of variables and circumstances involved in optimizing video for various delivery media and there is also the workflow process that has to be taken into account.
HTH
Roland Kahlenberg
https://www.broadcastGEMs.com
customizable animated backgrounds with Adobe After Effects project files