I advise you to try setting up the scan as usual in MP Navigator, only selecting 'Stack of Documents (ADF)' instead of 'Photos/Documents (platen)', at this point:
and load the documents in the ADF feeder on top of the printer, instead of onto the platen one by one (which inherently separates them into separate files.)
(If you are in one-click mode - which is less flexible - you will not have the above choice... so if your MP Navigator window looks small, like this:
then click once on the icon at the lower left of that window, to expand into the full options mode. Then proceed with the scanning of documents in the ADF...
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