It seems to me that the process was slightly different either over time or at different factories. Some are stapled but mine were held with a small nail. I started on the long runs inside and after removing the wooden trim which I subsequently cleaned up and put a light walnut stain on to restore the looks. Then I very carefully pried up the nails and removed them (I actually reused them as they were not rusted) and then used the old seal as a template for the new one.
Then I attacked the door seals and rear panel seals; and note that they were cut-out around the vertical tracks and copied those cut-outs to prevent as much drag when lowering the top as possible...you will need to do this elsewhere also!
After I had finished the inside I checked the up/down and noticed it was much smoother because the Pirelli seals centered the top and it helps to guide the top when it is lowered.
On the outside, I did the sides first and noted any cut-outs again and simply started at one end and ended at the other.
If you have a CO like mine, take a good look at how yours was constructed and try to determine if someone has tried to seal up the curved section before. Again, I think at different times or different builders did it slightly different. This is where soft/rotted wood can be found because the nails and/or screws used there will practically fall out and certainly won't grab when reinstalled. You are using stainless steel nails or screws to replace the old ones! I had good luck with the curve on my Alaskan but I chose SS screws a 1/4" longer and when I installed them they grabbed the old thread area just fine but when that last 1/4" was tightened they needed some torque to seat them....meaning no rot in there!
Don't forget the butyl seal and Pro-Flex as added protection on other places!
Oh yeah...I let the Pirelli seal sit in the sun a few minutes before installing as it is a bit more pliable then.
There are more threads here I think that may be much better than my feeble attempt here to explain it, but bottom line is, when you are done you can't see daylight when inside the Alaskan where the old shredded Pirelli was. I happened to go check mine with the top up one morning when it was 55F outside and it was still warmer from the sun the day before. Conversely, I left it closed all day and the temps were in the mid-high 80s and I found that it was a bit cooler inside.
Simply making it airtight as possible means warmer at night and cooler in the daytime.
Good luck!