It's always a good idea to try and capture audio and manipulate it at the highest practical bit depth and using the file format that degrades the quality the least. For that reason, either the WAVE or AIFF file format at 48 KHz, 16 bit or greater should be your goal. Audio on DSLRs is really an afterthought and not suitable, in my opinion for critical work. I always use a Zoom H4n recorder in tandem with my DSLR to avoid that issue. I synch the camera and the recorder with a slate (though you can use the headphone output of the Zoom recorder to link the two together.) The sound and audio can be joined in your NLE manually by lining up the audio waveforms or using software such as (Plural Eyes.) All of this takes a little extra time, but the results are so much better.
To go a bit deeper, professional audio for video is captured at 48 Khz in either 16 bit or 24 bit (the standards are AES and EBU, look 'em up if you like.http://en.wikipedia.org/wiki/AES3
) The higher bit depth helps a tiny bit with detail, but most folks can hardly hear the difference, just as it can be often be challenging to distinguish between visual images at 8 bit and 16 bit. Once you have done all the work you need to do, you can down-sample the audio to whatever format you need for your delivery needs.