Best settings for outputting to PowerPoint?

I'm very new to Motion. I would like to output an animated logo generated in Motion for use in the bottom corner of a corporate presentation using PowerPoint on a PC, preferably with a transparent background. Guidance/suggestions would be most appreciated.
Thank you.

I wouldn't create a movie that big just to have an animated logo in the bottom right.
What's the background like in that corner of the PPT presentation? If it's a solid color, simply make a Motion project just big enough for the logo animation itself and make the background of your Motion project the same color as the solid color of your PowerPoint background. Make it bigger than what you need, import it into PPT, scale it down to the size you want. Doing this means that if your presentation is played on a 1600 x 1200 or 1024 x 768 display, it will always look sharp and not get pixelated.
If your PowerPoint background is not solid, but textured, you take a screenshot of that corner (or export as a pict and crop in Photoshop) and then bring that into Motion and make the Motion project dimensions the same as the size of that screenshot. You then put your logo animation over that screenshot background. You then import that into PPT and line it up to the corner and you shouldn't see a seam.
By doing it this way, you don't have to have alpha channel support (does PowerPoint even support alpha channel?) You can now use H.264 as your codec and you'll end up with a very small file size.
Does this PPT presentation get distributed on Windows PCs or is it only used on your Mac? If it is distributed to Windows PC users, you will want to use Flip4Mac's software to make the QT movie a Windows WMV movie instead because every Windows PC can play that. Windows users will get a big red X at the bottom right where your QT movie is if they don't have QuickTime installed. To avoid this issue, I always end up making my videos WMV 9. The $49 version of Flip4Mac should be just fine for this use.
http://www.flip4mac.com/

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I?m recording some very machine intensi've video & sound to outboard devices. I'm using these outboard devices so that the recording process itself does not impact the demonstration performance.
Concerning the sound out, I?m using the line & 2 out of the card, and running it through a pro level audio board (Mackie) for any adjustments & monitoring before taking the line out of the board into the recording device. When returning the sound for monitoring, I?m also running from the external device directly to the board and directly from there to either headphones or control room monitors. Thus, I?m using the Audigy for initial sound generation. So far, I've not really made any ajustments at the board other than level or balance. I like to keep things pretty flat in recording.
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