TBH, "If I knew then what I know now", I would not have removed the scuttle panels. My car's 8 years old in a few weeks and I've realised that the external plastics are somewhat brittle, and I damaged one of the scuttle covers. Each of the two covers are held down by a rubber seal forward of the windscreen and a rubber seal around the bonnet hinge. The fragile part is on the underside of the cover where it meets the windscreen, and comprises a moulded lip (actually a protrusion) that sits in a groove at the base of the screen. I don't have any pictures of the underside of the cover, but I've posted an image of the base of my screen showing the groove. I suspect the reason you are finding it hard to remove the covers is that like mine, yours are full of crud that's been washed off the screen. This acts to clamp the lip into the groove and if you pull to hard, as I did, then the protrusion snaps off. So my left scuttle cover has half its protrusion missing and is now held to the right side with a self tapper.
So, what would I do differently? First, not remove the scuttle, and with it still in place I'd try to establish if I had a problem under that cover. Skoda calls that "the water box" and if I had my time over, I'd try to see if this was the source of my leak by pouring water in the drainage gaps, but colouring the water with food colouring. Then if you find coloured water in your cabin, you've got the source of the leak. Obvs something not to do if you have a cream interior carpet; mine are black!
Second, to test whether I had a windscreen leak, I would just cover the trim at the sides and the top with PVC tape to stop rain getting in. If the leak stops, then you've found the source of the leak and you'll need your screen sealing. (I recommend that if you do that, experiment with the tape on an inconspicuous part of the body, just in case the tape adhesive is too strong and you end up with a car in primer...) The stuff I used to seal my screen is not a car product as such, but is a flexible mastic/adhesive made by Everbuild and sold under the brand name of Stixall. It's available in DIY sheds and from auction sites, and is applied with a gun as you might use for silicone sealants. To get to where the side of the screen meets the body and to force the Stixall in the gaps, you'll need to take off the two trim stips at the side of the screen. Again, you need to be careful as they might be as brittle as mine and are expensive to replace! At the top of the screen, there's a simple rubber seal that sits in a groove and mine came out easily and went back more easily once it had been lubricated by Stixall. If ever I needed a new screen, I'm certain that the installer will have their work cut out to clean all the Stixall off the body, but I'll cross that bridge as and when.
The above is my story; there's no guarantee it will work for you. Caveat emptor and all that.
Have a poke around THIS website: (http://www.ilcats.ru/skoda/?function=getModels&market=CZ&language=en) . They have exploded diagrams of the Superb, and I found the pages very handy when I was trying to find how the body went together.
Stay Safe!