Getting your notes into the pages of a customized study Bible is a priority for the future. To do this each page of the Bible is laid out into areas that have scripture and areas that have 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.
A common use of the column headers in a two-column Bible is 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 column headers. BibleStudy.tools custom Bibles show chapter numbers in the two outer column headers and the two inner headers are currently blank, reserved for your chapter summaries. Use the "Chapter Summaries" panel from any of the pages that offer notes editing and write a few-word summary of a chapter. When you generate a custom Bible the inner column header of a page will show the short summary you've written for the chapter that's named in the outer column header of that page. The summaries can be written right now, but linking them into custom Bibles isn't ready yet.
A scheme for getting your other notes into the left and right margins (or possibly a center column) will be developed after your chapter summaries get into the column headers.