Setting the frame rate to 29.970 is the correct thing to do and should not affect the final out put. The software should just do a normal pull down that you shouldn't notice. What will the final delivery be of the documentary, DVD, BlueRay disk, YouTube, etc. this should be the main consideration when selecting a format to render. Then considerations like file size/quality ratio. ie small file less quality etc..
If you are going to burn it to a DVD use standard mpeg2, If you just want to up load to YouTube I have found .wmv is a good format to use as it is reasonable quality and a reasonable file size to up load. My favourite codec to use it the Main Concept mpeg2 with a HD resolution. I find this gives a better end product but a bigger file size. So I would recommend that you continue experimenting to see what works best for you.