I wouldn't soak the alder chips in anything. Wet chips just steam until they get dry enough to smoke, so you really aren't adding anything by soaking them. If you wanted to soak the fish in something before applying the glaze, go for it. Just make sure it isn't anything too acidic or you will cook the salmon in the marinade.

If you have a remote temperature probe, you can use it to cook the Salmon until done. Those fillets should be thick enough to get a probe in. Cook to an internal temperature of 140 degrees for moist, pink salmon. Anything over 150 and you are drying out the fish.