Can I manually check the box that needs to be selected in the patent application? Can I write the pages in the document list by hand?

Of course, you can manually tick the box, but the number of pages in the document list should be printed out. If you find individual errors when submitting, you can manually modify them. In short, it is not recommended to hand-write patent application documents, because once there is handwritten content, it is hard to say who changed it, and it is hard to blame if it is rewritten by others.