I had this same question and finally figured out today how to do this on my Canon MG5220 printer but I bet several printers are similar.
This is what I did. I scanned multiple pages on the flatbed and each scanned page showed up in software as a separate pdf image file.
Over on the left hand side of the screen I have an area called View and Use at the top of the screen. Down below there is a section called PDF.
Under PDF there is a tab called Create/Edit PDF file. Click on it. Select all the pages or separate pdf's that popped up previously. I checked the check boxes on each pdf in the bottom left. (This part I am basing on memory.) Another screen popped up with the pages. Only the first page was highlighted. I scrolled down and held the shift key and the last page to select all pages.
Then I clicked on the side of the screen under the pdf section that says "save all pages". Then I had the option to select where to save my pdf and the pdf was saved with multiple pages. Note: I don't know why but one page was out of order. I had to go back and repeat the process where I had selected the pages. Apparently one page had shifted in the final part of the process. All I had to do was click and drag the page back to where it should be and save all pages to a new pdf file again.
I hope this helps. Part of the reason I am documenting this is to help me remember the next time I try to do it.
