What are you planning on taping?
Generally, you want to plug the mics into the preamp, and plug preamp into the LINE Input on the R-09.
As for bitrate type settings, it depends on what your goal is, and what you're after. If you only have a 2 GB memory card, but you want to tape 2.5 hours or more at a single show, you will need to run at 16-bit. However, if you only need to record for 1 hour 50 minutes or less and have a 2 GB memory card, then you can go with the 24-bit setting.
If you have a 4 GB memory card, then you can get almost 4 hours at 24-bit, so it's a no brainer t run at 24-bit in this case (you'd likely go with 24-bit in this situation, unless you don't want to bother with dithering/resampling in post).
Several people have mentioned that using the "AGC" on the R-09 is not a good idea. So you should probably turn that switch to the "OFF" position.