To add to what slipperybidness states above (i.e., bypass the subwoofer crossover if possible, otherwise set it at its highest frequency setting and use the receiver's crossover), since the -3dB point on your main speakers is 40 Hz, you will want to set the receiver's crossover above that. You may want to try 60 or 80 Hz. Which is more appropriate depends on what subwoofer you have, and how loud you play things (basically, the higher the frequency setting, the lower the demand on the main speakers' woofers, so they will play louder with less distortion at a higher setting, but the subwoofer then must deal with those frequencies below whatever setting you select).
The automatic setup can be used for the levels and delays.