If you're going to move them from one wheelchair to another then you'd need staff trained in suitable lifting and handling techniques and possibly a hoist to move them from one to another. Also, some people need quite specialist wheelchairs.
You search the person just like anyone else as much as it practical. If you're searching bits they can't feel then you should tell them what you're doing ie. "I'm going to pat down your right leg, I'm just checking around your shoe" etc. The wheelchair should be treated carefully as they see it as a part of themselves to some extent. But there is no real way of searching the tubular frame. If there's a possibility of explosives then your only option really is to use dogs. The detection machines tend to give false positives for things like WD40.
Thanks for your advice. We have a set up like an airport, however we dont normally deal with wheelchair users, so am in need of best practive. Our main worry would be what could be inside the frame of the chair.