So it would be three positions, Bridge, Bridge + Neck, Neck?
That will work fine. your rotary switch will probably have 4 inner lugs, one for each pole, and 12 outer lugs being 3 lug connections for each pole. You should identify which lugs connect to each pole, visually or with a meter. They should be the 3 nearest outer ones for each inner pole.
call the inner poles 1, 2, 3 and 4
call the outer lugs 1A, 1B, 1C, 2A, 2B....etc corresponding to three switch positions A, B and C
You only need two poles, so ignore half the switch
Wire your pickups: ground to guitar ground, bridge hot to Pole 1 and neck hot to Pole 2
run a wire that connects these four outer lugs, 1A to 1B to 2B to 2C and then to the volume control for output
thats it!
John