To get your notes into the pages of your custom study Bibles, each page of the Bible is laid out into areas that have scripture and areas that allow notes. All Bibles are two-column, so each page has left and right columns for scripture, left and right column headers above the scripture columns, and left and right margins outside the scripture columns. (The bottom of a page isn't targeted for notes, but might be used for other things, like a page number or a chapter counter.) Pages are then laid out next to each other in standard book fashion, where the first page stands alone and then all other pages are seen in pairs, called "facing pages." When a printed book is laid open you see two pages, a left page and a right page, and that's how the PDFs are laid out.
It's common in a two-column Bible to put the chapter number in the two outer column headers of a facing-page pair, and to put some short summary of the text in the two inner headers. BibleStudy.tools Bibles show chapter numbers in the two outer headers, and the two inner headers are reserved for your chapter summaries. Use the "Chapter Summaries" panel from any page that offers notes editing to write a few-word summary of a chapter, and when you generate a custom Bible, the inner header of a page will be the summary you've written for the chapter that's named in the outer header of that page.
A scheme for getting your other notes into the left and right margins (or possibly a center column) is planned for the future. Cross references to other Bible passages or to your own notes and studies will help you keep your Bible understanding at your fingertips.