as said above, the sub needs an enclosed area to create pressure. "volume" on a sub is spl (sound pressure level). the smaller the space the more pressure it can create and the louder it will appear to sound.
in regards to the origonal question; the bass control on the headunit is just that. it controls all bass and is not an independant sub control. if you are wanting to control it seperately then you can put in an equalizer to seperate the output signal levels between speakers and sub. the other option is to put something like a bass blocker on the seakers to keep them from playing bass. a fairly simple and inexpensive route, but is not the recommended fix. these are simple devices that eliminate all frequencies below a certain point (usually 220hz) you will loose some mid bass as well as bass. the sub doesn't play high enough to cover that gap (usually cut off about 80 hz) so there is a range that will not be played at all.
2010 Volvo C70
2011 Harley FLHTK
Midwest Crew #22