Which way was the original before you took it off ?
For now I would put it on the way the old one was, at this point to save yourself some heart ache down the road ,screw the well in place with some self tapping sheetmetal screws for now. Set your quarter panel in place holding it with some vise grips. Now you should be able to see where you want to place the wheel well.
Whether that lip is going to be on the inside or outside of the inner panel to me don't matter as much as getting that wheel well to partner up with the quarter.
If you can, install the fender and door on that side also, this will help with proper alignment of quarter.
You got to remember, you are working with aftermaket parts.
Ain't no how, no way they are going to fit like OEM parts without a bunch of cussing,tweeking and cheating.