In order for Network Manager to use the USB device, find out what the driver is for your internal and blacklist it. Learn the driver with:
sudo lshw -C network
For example,on my machine, I see:
description: Wireless interface
product: Centrino Advanced-N 6200
vendor: Intel Corporation
<snip> driver=iwlwifi driverversion=3.5.0-25-generic firmware=220.127.116.11 <snip>
So, if I wanted to disable my internal, I'd blacklist iwlwifi.
echo "blacklist iwlwifi" >> /etc/modprobe.d/blacklist.conf
modprobe -r iwlwifi
Then the USB, using the built-in driver rt2800usb, should work fine.
Of course, if the internal is not working as expected, we could troubleshoot it.