There are no conflicts between the two, since they are separate product lines. As for your other issue - LR is basicalyl ACR. If it doesn't open your RAW files, they may not be supported and in that case you are not solving naything by switching to PSE - it uses the same ACR stuff or even usualyl is one or two .x versions behind. Refer to these lists:
Camera Raw plug-in | Supported cameras
Camera Raw-compatible Adobe applications
Mylenium