Because the old, flimsy skylight was a rectangular shape and the new skylight was an oval shape, the interior part would not fit properly. Once you remove the interior part you'll see that the roof is about an inch thicker on one side than the other. I measured each corner and used a cutting wheel to trim off the inside part. I then bought a piece of plexi-glass and glued & chaulked it together- actually looks pretty good.
My replacement skylight was pre-drilled, but the holes lined up! The only holes I had to drill were for the seam screws to go thru the skylight. Make sure you use flat-head/sheetmetal screws and don't over tighten them to prevent the skylight from cracking!
Did I mention removing those screws under the seam are a Royal PITA!!
**Have plenty of adult beverages handy and no-one nearby that might be offended by profanity!