Are you using Soundtrack Pro 2?
First of all, I assume you are editing a multitrack project and not an audio file, right? There should be a "File -> Export..." option. Look at page 396, chapter 16, of the Soundtrack Pro user's guide for details; the short version is that from this export dialog, you can create multiple mono files (such as 6 files for a 5.1 mix) and turn them into an AC3 file (Dolby Digital, stereo or 5.1) using Compressor, or use "Exporting a Master Mix to a Compressed Audio File" to do this all in one step.
Either way, what you do is encode your audio using Dolby Digital (AC3) for DVD Studio Pro. You can use uncompressed AIFFs in DVD Studio, but they use a lot of the available space on the DVD, and unless you have specific reasons to go that route it is usually recommended to encode Dolby Digital, even if it's just stereo.
Hope this helps!
- Martin