The Edirol R09 can only record from one source at a time. So you either have to record via the 1/8 mic/line inputs or by the built in internal mics.
As far as I know the Zoom H4n is the only sub $400 recorder that has multiple input capability (internal mic and XLR inputs).
If you want a recorder from Edirol that has multi channel/input recording then you have to step up to the Edirol R44, which records 4 tracks via it's 4 XLR inputs. But you can also record 2 channels via teh internal mics along with 2 of the XLR inputs.
The Zoom recorders aren't bad for most uses, but they have fallen short in the past with it's built in pre amps. Supposedly the new new H4n has improved low noise pre amps, and reports seem to back that up. But how quiet they are compared to better units from Tascam, Edirol, Marantz etc. is still to be seen, or rather heard by me.
Suprisingly I might be selling off my Edirol R44, as I am not getting as much usage out of it that I would like. I find myself using smlller recorders liek the Marantz PMD620, Edirol R09, Zoom H2 more so. I may be selling off the 4 track R44 for a Zoom H4n. I know the fidelity won't be nearly as good as the Edirol R44, but the smaller form factor and ability to record via XLR inputs and built in mics are much more appealing to me for my video/audio needs. Which I normally like to record live events that I shoot (weddings/stage etc.) by attaching multiple mics to a mic stand and micing a source, like a PA system, and also use a stereo mic to record audience noise. The H4n suits my needs better, due to it's smaller size in that I can attach the recorder facing the audience to record crowd reaction via it's built in mics, while using 2 Rode M3 mics to mic the PA or band for a 4 track mix. For the R44 I have to leave the recorder in a bag attached at the base of the mic stand and run cables to my inputs. This setup takes me much more time to setup and leaves me less time to focus on my video production.