Well, the way that I usually do this personally, is this:
1. Solo the midi tracks you want to export to audio. 2. Set L and R locators to start and end of the project. 3. Go to File, Export, Audio Mixdown. 4. In the export dialog, choose the same file type as your project, select the project folder to save it to, and then choose the option "Import to Audio Track." This will automatically check the pool button, and that is ok. 5. Hit export and then you will have a new track with the audio file. Mute the midi track after this, so you don't get doubled notes.