That was thought for "real" instruments, like Digital Piano. So the same "notes" can be used for playing as well as for commands. But than Sonar has to distinguish these 2 cases, so you should define some "Shift" button in "MIDI 'Shift' Options" (the same page in Preferences) and use combinations of Shift + Pad.
In case you want use APC as a Control Surface, you should configure it as such (see chapter 40 in the Sonar Reference Guide).