Why a visual organizer helps
Scans rarely come out in the right order. A feeder jams, someone scans the back of a sheet first, or you add a late page at the end. Dragging thumbnails is far easier than guessing page numbers, because you can see which page is which.
The same applies to presentations exported to PDF and to documents assembled from several sources, where an appendix needs to move up front.
Think of it as laying paper pages on a table. You can see the cover, the contents and the appendix at once, and you move them with your hand rather than a number.
Working with a big document
For a long file, work in passes. First delete anything obviously unneeded so the grid gets smaller. Then move the largest blocks into place, such as the cover and contents, followed by the finer adjustments.
Thumbnails are generated in your browser, so a 200 page file may take a moment to load on a modest phone. Rotating a sideways scan from the thumbnail view fixes it for the whole output, which is handy when a stack was scanned in mixed orientations.
Give yourself a clear goal before you begin, such as contents after the cover, appendices last. Write the order on paper if it is complicated. It is easy to lose track when a hundred thumbnails look alike.
Save intermediate versions if the changes are big. A copy named v1 before you start the second round of reordering gives you something to go back to.
Organizing across several files
To mix pages from two or more PDFs, merge them first in the order that is closest to what you want, then open the merged file here for the detailed rearranging. This two-step approach is more predictable than trying to interleave files in one pass.
When you are done, check the first and last pages and any page you moved. Mistakes tend to show up near the boundaries.
The same approach works for a photo album built from a PDF. Combine the files, then arrange the pages so the story reads left to right, top to bottom, which is how most people scan a grid.
What is preserved
Pages are copied and rearranged, not re-rendered, so text remains searchable and sharp. Internal links that point to a page you moved may not follow it, so test any table of contents links after reordering. Encrypted PDFs and files over 100 MB are not supported.
Page sizes and orientations are also kept, so a mixed bundle of portrait and landscape sheets stays that way. Annotations and form fields attached to a page travel with it.
After saving, open the new file in your usual PDF reader and page through it once. Check headers and footers, because a running page number printed on each page will not renumber itself when you move the page. If that matters, use the add page numbers tool on the final order.