Most people prefer to have their subwoofer handle all bass, relieving the main speakers of the job. Each speaker you identify as small has the bass extracted and sent to the subwoofer. The LFE (bass sound effects) channel from multi-channel sources (e.g., Dolby Digital 5.1) will also be sent to the subwoofer.
So start by identifying ALL of your speakers as small.
The crossover setting adjusts how the receiver decides what bass to send to the subwoofer. A good starting point is 80Hz, and that is likely what your STD setting does, but see if your manual gives you more guidance. 80Hz is the crossover point mandated by THX standards.
One rule of thumb is to set the crossover at twice the lowest frequency spec'ed for your main speakers. But you don't really want it to get set much above or below 80Hz or you will likely run into problems. A range from 60Hz to 120Hz should be about the limit of what you try.
Meanwhile, since the receiver is already doing this crossover stuff, you want to get the crossover built in to the subwoofer out of the way. With some subwoofers you can disable the crossover or use an input that doesn't process the signal through the crossover. Failing that, turn the crossover on your subwoofer to the highest possible frequency.
After adjusting crossovers, re-check the volume balance for all your speakers and then do some listening. This setup may work fine for you, but feel free to play around.
With bass test tones at various frequencies -- available in some receivers but also available from calibration DVDs like Avia or Digital Video Essentials (DVE) -- you can see how bass response is going up and down according to frequency.
Moving your subwoofer a bit, adjusting polarity and phase, or changing the sound configuration of your room (closing doors, pulling curtains, adding stuff to the walls) can all affect bass response quite a bit.
Polarity and Phase can be very important. They adjust the relative motion of the subwoofer and main speaker drivers so that the two of them aren't cancelling each other out -- particularly in the vicinity of the crossover frequency.
A Sound Pressure Level (SPL) meter -- the one sold by Radio Shack is the one everyone uses -- will help you measure these variations more precisely.