Use "Gold Gulch Parking Lot" for the destination, and they can drop you off right at the lower gate entrance. (There is a turn around spot a few hundred feet past this entrance, or in the parking lot.)
We recommend parking in the Organ Pavilion parking lot: Pan American E Rd, San Diego, CA 92101 This is now paid parking, $10 for four hours or $16 for the whole day. Even though this lot is near the Upper Garden entrance, you can walk or use the provided shuttle down Paseo de Oro to enter at the Lower Garden gate.