well I haven't faced this problem, and you can actually control that which track you need to export and which not! By the way here is my way for exporting a video together with audio track in a single file,
after I finished with my composition and adjusted the work area using the timeline work area bar, I go to Composition > Make movie
Then your request will be added under 'Render Queue' which you can simply set all the settings due to your demand.
But usually exporting media in 2 different files happens when you choose MPEG file compression, in that case AE or PR gives you an .m2v and a .wav file if i am not mistaken which then you may need another software to compile them together. So to avoid that, yet getting an MPEG file format in your output you need to check 'Multiplex DVD' radio-button under the Audio settings of the menu!
Hope this can help you.