To get the best balance of sounds in Box Of Stops, typically you will want to disable Local Control on your keyboard.
If Local Control is enabled, this means you will be hearing another sound, often a piano, generated by the keyboard for itself. Also, Box Of Stops generally doesn't use the full channel volume available for each instrument, so the locally controlled channel may dominate the sound.
This is not say that it is always wrong to leave Local Control enabled though. With some keyboards the locally controlled sound is independent of the normal limit of 16 Midi channels - it effectively gives you an extra stop on the organ. Also, if you are experiencing Latency problems, the locally controlled channel will typically be the quickest responding channel, giving you more control.
Setting Local Control
This will depend on the individual keyboard.
Typically a higher end keyboard has a control panel. Local Control will be a setting on this, often in such as the Midi menu.
Otherwise it is usually a case of taking a look in the User Manual for a relatively arcane key sequence. For example with a Roland digital piano you must press Metronome+Reverb together and B7 or C8 to toggle local control off or on respectively. Similarly for a Yamaha Clavinova you press Demo+Piano together and then C6 toggles both ways.