Just place the .ISO or .WBFS file you have in a folder called wbfs on the SD Card. USB Loader will read from that.
No need to delete anything from the SD Card.
^ Nope. When you sync an out of region gamepad controller to the wii u it asks you to do a GamePad Update and then fails because you can't do an update with an out of region GamePad.
Verified with my USA and AUS WiiU's