I have had these for a while now and finally decided to decorate them. I know you have questions so here are the answers. Yes, I covered the pen, yes, it was a pain in the neck, and yes there is a seem. I don't know if you can do it with out having one. The pen doesn't come apart so I couldn't take off the clicker part. If I could have it would have been way easier.
For the cover and the pen I used Mod Podge. That stuff dries in like 10-15 minutes so it is easy to crank these out.
I painted on the Mod Podge on the cover of the notepad and put the DP on, then rubbed my hands on it to smooth it down, then painted Mod Podge all over the DP. For the pen, I painted Mod Podge on the back of the paper and wrapped it around the barrel of the pen, then painted Mod Podge on the paper. I also ran my finger along the seem to make sure it won't come apart.
If you are planning on doing some of your own let me save you the time of measuring. However, you might want to cut a piece of copy paper and match it up to the cover of the notepad just to make sure before you cut into your designer paper. That is what I did and I noticed that one of the four books was a little longer so I was glad that I didn't cut my paper too short. For the cover, I cut the paper 5 x 7 13/16 and the paper for the pen is 3 1/2 x 1 7/16
Paper: Basic Grey, Fancy Pants DP, DCWV,
Accessories: Mod Podge Matte (in the yellow bottle, Foam Brush, Target Notebook With Pen