I think you can make a folder, and direct files to it. I guess I'm just used to working with the Edirol R4-Pro, what makes a new folder by default for every take. Not too big of a deal I guess.
On another note I did an A-B test with 5 different mics yesterday. I played guitar through a mic plugged straight in to the DR-680, then again going through the MixPre and into the 680. I recorded and filmed the tests, and will be making a shootout video of sorts to illustrate the effects of the MixPre on the mics. I chose video because I can get pretty good audio using Vimeo, and to be able to put up text to show what mic/mixer is being played through is much easier to get a seamless A-B comparison. In most cases I think I liked the DR-680 pres better than the MixPres. The MixPre seemed to suck out the fullness of the signal. I say "seemed" because I need to dig into it and level match all the takes before I decide for myself. But my preliminary results show a lack of low end with the MixPre. It was most pronounced with the Rode NT4 though.