If you can't follow the guide you may need to contact Visioneer.
If you are doing separate jobs it makes separate files. You can try to get one file via Manual Feed Mode (Page 21 of OneTouch guide)
If you are loading 5 pages in the adf and getting 5 pages in separate digital files, then you are using single page formats or have Create single image files enabled (Page 16 of OneTouch guide)
Outside of those 2 options you would likely need Nuance Paperport.
We got a xerox documate 3220 and we're trying to scan multiple pages into one single pdf. Don't know how to customize anything from the scan window. The way it is now is that it's saving every paper scanned into its own individual pdf.