Yes you can. I've ran into 3 major US airlines so far. Flew NWA, was booked through United Airlines (flown by LH, but as it was a UA flightnumber for the flight in, that was under their rules) and at the moment booked on Continental. All 3 of them allow you to take both free of charge. One checked and one gate checked.
I always fly with both my powerchair and manual chair. One reason is the 'you never know what they end up damaging this time' motive, another major reason is the fact that at my home airport I have to check in my powerchair at the check in desk. Also there is no direct flight to MCO from here, so when connecting to flight 2, I use my manual chair.
And if anyone ever has the urge to fly to Europe; we've got regulation on this subject since last summer. On ALL flights departing in, arriving in and/or connecting within the EU, you are allowed to check in upto 2 mobility devices (which can mean 2 wheelchairs) free of charge. Not all airlines seem to be aware though, so be prepared. They used to charge you the overweight fee for a second chair, which could get really expensive.
BUT! Be aware; flying with 2 chairs also means the risk of having 2 chairs ending up damaged, misplaced etc. One would think the odds would be against such a thing happening on one trip, but since my last flight I no longer count on statistics to much.

For me personally this doesn't outweigh my personal benefits of travelling with 2 chairs, but for others it might.