I changed a gear box and now my steering wheel is off center. Can I adjust the tie rods to center the wheel without screwing up my alignment? If so, how?

Not sure what vehicle you have, but I just did this on my 72 Chevelle.
If you disconnect the intermediate shaft, you can align the steering wheel.
The intermediate shaft connects the steering shaft(the shaft that goes through the firewall) to the steering box, you can then align the steering wheel to the intermediate shaft splines and reinstall.
What I did was, put a tie wrap on steering wheel ring, centered, this way I could see the wheel from engine bay and know when position it was at while working on the shafts. Then I disconnected the intermediate shaft from flex coupling at steering box, 2 bolts. Compress towards firewall and it clears enough to dislodge from coupler. Then I took pinch bolt off where intermediate shaft connects to steering shaft, near firewall. After takeing the bolt out, you should be able to pull the intermediate shaft off the spline. It may be a little tight, you can spread the clamp a little and it should slip off.
You can also mark the two shafts if you want and use the marks in conjunction with the tie wrap to see how much you are adjusting. After seperating the shafts, you can freely turn the steering wheel to align to steerg box.
Reconnect after aligning, start all the bolts, but don't tighten fully yet. Start car and see if everything stays aligned after turning the wheel a few times. I have more play in mine, so it took a few times. If everything cks out, tighten all the bolts and your done.
Note: The spline connection where the pinch bolt goes in has a recess that you have to be aware of. This allows the bolt to align with the clamp correctly. If you don't have it aligned with the recess on shaft, the bolt will not pass through the clamp to where you can put a nut on it.
Hope this helps. Someone may have an easier answer for you, but this is what worked for me. Only takes about 20 minutes.

It is imprortant that the steering wheel is at the centered position when the pitman arm is pointed straight ahead. If you get it straight but the pitman arm is off center then your center to lock turns will be different for right and left turns.

This paper covers steering gear and steering wheel centering for cars with intermediate steering shafts.

http://www.corvettefaq.com/acar/SteeringWheelCenteringA-Car2ndGenF-Car.doc