is an excellent guide to numerous ways of converting a multipage document scan into a PDF.
Basically, you scan your pages into multiple files, e.g., scanxx.jpg where xx is a sequential number.
Then you have several choices as detailed in the article.
1. The simplest is simply
convert image*.jpg image.pdf
I haven't tried that, but the one I did try was to import the images as layers into gimp, save the lot as an mpng file, then at the command line use
convert image.mpng image.pdf
I won't steal Patrick's thunder so check out the link for details.