On the subwoofer, bypass the internal crossover if possible; if not, set it at the highest frequency. The subwoofer volume level you will probably want to try would be about midway up (you will be using the receiver's settings to balance the sound, though if the receiver sets the sub out level much different from "0", you will probably want to change the level and rerun the calibration in your receiver; if the level is much higher than 0 for sub out on the receiver, turn the level up on the subwoofer and rerun the calibration; if it is much lower than 0 for sub out on the receiver, turn the level down on the subwoofer and rerun the calibration).
Your subwoofer also has some customizable settings, and you will want to bypass any extra processing before running the calibration on the receiver. Later, if you want to apply the customization, you may do so, though you will be altering the frequency response from what was originally intended (which should be done if you like it, and not if you don't).
After carefully placing your speakers, you want to run the room calibration that your receiver can do (that is the calibration I am referring to in the parenthetical remarks above); see its manual for how.
You will probably want your speakers set to "small", and the crossover should be set where you like it best between 40-80Hz; I recommend trying different settings on that, but keep in mind, each time you change that, you will want to rerun your calibration of your receiver for the comparisons so that it sets everything properly for that setting. If you don't want to bother with that, just pick 60-80 Hz with those speakers and be done with it. If later, however, you add smaller rear speakers, you will probably want to run those at a higher cutoff frequency (if you buy decent rear speakers, probably 80 Hz).
As far as the various processing settings go, you may set them as you wish; you may or may not like what they do with the sound. If you want to just hear the music as it is on your discs, set your receiver to "straight" or "bypass", but check your manual to make sure it does not remove the subwoofer from being used that way, if you want the deepest bass in the music. If it does cut out the subwoofer, select "stereo" for CDs and other stereo music to play it without extra processing.