External mic only recording on left/right side

Boy, I'm having audio issue after audio issue with iMovie. The problem now is that I want a better audio quality than mic built-in microphone so I'm recording through a two-channel Focusrite audio interface. iMovie reads the interface just fine, but will only send the signal to the left or right (depending on what input on the interface I'm using). When using the built-in microphone, it records stereo just fine. But, again, I'm wanting to use a better microphone. Help please!