Conflict between Acer's Atheros and Linksys wireless USB

My Acer Aspire One is only 2 weeks old and I just finished setting it back to the factory defaults.
I don't know how I screwed up the Atheros wireless but I did. It would only give me that
(limited connectivity) business no matter where I tired it. A complete reinstall to the factory
defaults is all that would work. I'm new to wireless and I am hot to trot on trying some high gain
parabolic antennas on 2.4 GHz and inorder to do that I bought a Linksys USB adaptor because
the Acer's antenna is tucked away behind the screen ( I THINK)... Because of the problems
I have already had with wireless I'm actually afraid to load the software and plug this wireless
adaptor in. I'm afraid of somekind of conflict between the onboard Atheros wireless package
and the USB adaptor. Could someone put me on the right track here? I'm thinking maybe
disabling the Atheros in the device manager but that
sounds to easy. Then to with my luck it might not turn back on again because of something
the Linksys software changed. This may be one of those just to many possible outcomes
so just do it and see what happens.
Thanks for any insight..........
Mike