If you scan a bunch of stacked pages they will be made part of a single PDF. If you scan pages separately for some reason then simply combine them in Preview.
The Fujitsu scanners are awesome; I've been using the S1300 for almost a year. Don't even bother looking at the competition; I did a careful review and the Fujitsu easily won the race.
I also second the DEVONthink recommendation. It is simply the most powerful database app out there. I've used DT for around five years and it has never given me a lick of trouble. I do biomedical research and regularly ingest Web pages, PDFs, scanned articles... you name it. I currently have around 3,000 studies and articles in DT. No way could I manage or get full use of all that data using a Finder-based filing system. DT's artificial intelligence is the key to DT's sophisticated search functions. It can also display almost any file type without having to open other applications.
The main difference between DT Personal and DT Pro and Pro office is the ability to create and open multiple databases. The primary differences between Pro and Office is that you can archive most e-mail, Office has a built-in server and you can scan directly to Office via a Fujitsu scanner.
I don't need e-mail archiving (it doesn't work with GyazMail anyway...) and I don't need to scan directly to DT. There are myriad ways to move documents into DT so I don't see the point unless you plan on scanning a ton of docs that will ultimately wind up in DT anyway. The reason I upgraded to Pro is for the multiple databases.
Devon technologies is close to introducing a syncing system that will allow syncing of databases across multiple Macs. That will be icing on the cake for an incredible program that doesn't get the attention it deserves.
DEVONthink has a 150 hour demo period. The excellent "Take Control of DEVONthink 2.0" is a must-have for getting up and running quickly while taking full advantage of everything DT has to offer. If you don't require the features in the Pro versions the Personal version is an excellent deal. DEVONthink is regularly available at a discount in Mac bundles and every year around Thanksgiving it is available at a 25% discount.