OUCH! To answer your question I'm pretty sure the PE automatically transfers all of your apps to the MicroSD card when you install it, using the built in storage for system files only (effectively making the vast majority of the built in storage useless from then on).
I'm pretty sure the general consensus is to not bother with the MicroSD card unless you manage to fill up the internal storage because of this exact reason.
I'm not 100% on how it works exactly as I'm as new to this as you are. I read a couple of threads about it but that was before I had any kind of idea as to how Droid's (linux's) file system works...
|