I guess I should have been a bit more specific. I hinted at it, but never actually said it. Here is my set up:
Primary: Left
Secondary: Right

If I set the following, everything works fine on my primary monitor, but the popups on the secondary open to the left in an attempt to get onto the primary monitor.
xPopupScreenX 0
xPopupScreenY 0
xPopupScreenWidth $ResolutionX$
xPopupScreenHeight $ResolutionY$

If I don't set the values, the popups will treat my monitors as if they are one and open up using both screens. I want the popups to stay on the screens where I open them.