I believe it should be your primary residence. NSC would determine which local office based on the address you provide. Also, you will have to, sometimes, prove that you have lived at the address atleast for 3 months - during interview.
Also remember INS now-a-days is strict about not reporting address changes. If you use the secondary address, and INS finds out that the address you provided is NOT your primary residence, you might get into serious trouble.