Here's what I do on my wife's Jamis w/ BB5's. They need realigned often since you do minute adjustments for pad wear via the adjustable inboard pad adjustment and pulling more cable.
Ensure the wheel is completely in the drop outs and properly secured with the QR. Loosen the cable clamp on the outside and back the adjustable inboard (spoke side) pad as far out as it will go (away from the rotor toward the spokes... assuming you still have good pads left). Loosen the allen bolts attaching the caliper and slide it into adjustment using a business card as a spacer between the rotor and inboard pad. Tighten the allen bolts, spin the wheel to check for rub. If there's no rub and only a very slight gap between the pad and rotor you can now go to the outboard via the cable and adjust it tighter to bring the outboard pad as close as possible to the rotor without rubbing. Tighten the cable clamp and you should have tight, quiet brakes. That's how I do it for any mechanical brakes that don't have both inboard & outboard adjustments, hope that helps. Don't forget to back your barrel adjusters at both the caliper and brake lever all the way back to absolute zero before doing anything...if you're the type of person that uses them to fine tune brakes. They should only be used on the trail for quick adjustment, when at home, zero them out before tuning anything.