With MorphOS, you don't even have to have run UAE. Simply plug in your CF or SD card and off you go. The only thing you gotta watch out for is that you don't have the same directory names on your Amiga drive as you do in MorphOS.
I.E. My MorphOS partition is named "System" as is my Amiga OS partition. So when I plug in my SD card, my Amiga System directory cancels out my MorphOS system directory until I unplug it.