up in the left top corner you have settings --> options --> on the next window there is 4 check boxes, under them are where you link the LP to where your SWGEmu install is. Any issues after that usually get fixed with a full scan. At least it have for me.
Your profile is not dependent on the LP or LPE, it will be in the same spot on both. For me that is C:\Games\SWGEmu\profiles. I always take a backup on my profiles folder though, never know what happens and writing all the macros again is no fun at all.