In Ipad Pro this is what I see when I open the application:


On the comic folders there is a small black box in the middle, but it doesn't contain anything. What is it for? I guess it's an application error.
On the other hand, how does it mark when all the comics in a folder are read?

That “black box” is part of the folder icon, that icon represents a comic box. Look for “comic box” in google and you will get it.

To mark all comics read in a folder, select the firt comic using a right to left swipe and then select the lastest one twice, then long tap and set as read.