It's not that simple, actually. First of all, you shouldn't use AE for transcoding between PAL and NTSC material, at least not without some sort of plugin. There's no good built-in function in After Effects to convert frame rates.
First of all, you need to rip the DVD's assets to a real-frame file (QuickTime, if you're on a Mac). This will result in a PAL format file, of course - you shouldn't transcode yet.
Then, if using Final Cut Pro, invest in
Natress' standards conversion plugins. They are just $100 USD, often paid for with just one project. You'll use the plugin as an effect in Final Cut Pro to convert the PAL QT file into an NTSC QT file in an NTSC sequence.
Then, you'll need to take the resulting QT material and encode that to DVD assets (MPEG2 for video and AC3 for audio).
So, it's not just a simple one-step process where you convert a PAL DVD into an NTSC one. Although you
can do it in fewer steps, you don't want to, since the results will be poor quality video.