Bass cut OFF (if too bass heavy, EQ it afterwards for better, less drastic, more predicatable results)
Plug-in power OFF(when using battery box, ON if no batt box)
Mic gain HIGH/LOW depends on the sound pressure level of what you are recording (generally for loud stuff LOW, for quiet stuff HIGH)
Start with the mic gain set to LOW. Adjust the input level so the highest peaks on the meters land around -12dBFS (to allow some headroom for possible louder peaks without clipping). If you cannot get levels high enough to peak around -12, switch the gain setting to HIGH and readjust input levels. If you can get levels high enough but are near the top of the adjustable range, you may also want to switch gain setting to HIGH if allows you to keep the input level setting closer to the center of the available range.
Warning: In either case, there is a do-not-go-below input level setting. I can't recall exactly what it is on the R-09HR since I never used that recorder, but its total input level number range is something like 0-50 if I recall correctly, and that's different than the original R-09 which has an input level range of 0-30. On the original R-09, the do-not-go-below input level setting is 9, regardless of the HIGH/LOW gain switch setting. At settings below that the meters will not show peaking and the peak light will not activate, even though the recorder may be severely overloading, resulting in a distorted recording.
Someone will probably post the do-not-go-below input level setting for the HR, or you can use the search function to find the Edirol/Roland R-09HR user thread where you can find that information.