Splitting is the easy half. Separator sheets or blank pages tell ScanRoute where each document starts. The free printable separator sheets on the product page work for this today: print them at actual size, set the separator prefix to SR- in Settings, and scan a short test stack before a real one. The harder half is naming, because the name comes from one zone you draw, read on the first content page of each document. Separator pages are never used for the zone.
Pick a line that repeats. The zone is a fixed rectangle, so it reads the same spot on every document. Choose a line that is printed in the same position on every first page, holds the values you want in the name, and is typed rather than written in by pen. On a bill of lading your own office issues, that could be a header line such as BOL 2026-09-14 LD-48213. A pattern pulls Type, Date, and Load from that line, and each field is checked. Set the Load field to digits and a read that comes back with a letter O where a zero belongs fails the check, and the document waits for you instead of filing under the wrong load.
Keep the zone tight. Draw the rectangle around that one line with a small margin. A zone that sweeps in a logo, a barcode, or a signature block gives the pattern extra text to trip over, and the read is more likely to fail its checks.
When the layout changes from shipper to shipper. One zone cannot follow a number that moves around the page. Two honest options work. Accept that those documents will wait in the inbox, where you type the load number while looking at the zone crop. Or place your own load sheet, printed from your dispatch system with the load number in a fixed spot, on top of each load's paperwork, and put separators between loads rather than between documents. Each PDF then holds one complete load, and the zone always lands on your sheet.
Build the name around the load. A template such as {Load}\{Type}_{Date}.pdf creates a folder per load number and puts the BOL and POD side by side inside it. If two documents would get the same name, for example two delivery receipts for one load on one day, both are flagged as duplicates in the inbox rather than one replacing the other. Fix one name there, or add a field to the template that tells them apart.
Check before you bill. OCR and barcodes can misread, so Preview lists every proposed name and folder before anything is written, and only documents marked ready are committed. When the list looks right, commit. ScanRoute writes the named PDFs into the destination folder, leaves the original scan exactly as the copier saved it, and adds a CSV manifest listing every file with its SHA-256 hash.