For duplex scanning there is an option in the acquire -> start wizard window. In there the option is located right above the brightness setting and right under the paper size. Ticking this box will scan both sides of your document and will display them on two different pages in paperscan. If you still can't see this option make sure your paperscan pro is up to date.
For saving multipages, unless you manually save each page one by one after scanning each of them then you cannot do what you asked. For an alternative solution, the separator sheet is an option but isn't always the most effective solution. If you need to save multipages containing always a set amount of pages you can use the "Save X page(s) to file" which will automatically save files containing the amount of pages you set.
I hope this helped. If you have any further questions do not hesitate to ask.
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