What I would do is crop the bottom of all the pages from 11" to 3.5".
Then you can view the pages continously.
If you insist on having each page showing the front and back of one cheque, there are a few ways to go about it.
1) make an 8.5" X 11" photocopy of the front of each cheque and then stick the cheque at the bottom of the copy with the back showing and make your scan.
2) scan to TIF or JPG and do your editing in and image editor, combining the front and back of each and then print to PDF.
3) Maybe Acrobat 6.01 has a feature for this that I might not be aware of.