Here's the thing. With a document feeder you don't have all the activity you would have with a flat glass scanner. I load 30 pages in the feeder, set my Irfanview (which will work with many different scanners - you don't have to use the software that came with your scanner you know.) Anyway, I set my Irfanview Acquire dialog this way for example -
Now the file naming is automatic as is the page numbering. The pages here will be called 198309 Creative Computing - for Sept of 1983 issue and the page numbering will start at 1 and increment to 3, 5, 7, etc. As each page is scanned and sent to the output tray I pick it up and turn it over stacking for the flip side. When the magazine is done I can scan the other side and I simple change the dialog box starting page to 2 and they will then number 2, 4, 6, 8, etc. I use 3 digits to insure a proper page sort. When the magazine is done I will have my Creative Computing magazine pages in proper order and numbered right. Then I simply rar the pages into one big file and with Comic Book reader installed I change the rar extension to cbr and I have my book.
As you can see in the following picture there can be some bleed through if the following page has some dark areas, but I haven't found it to be objectionable at all. It really depends on the magazine. Some have some pretty thin pages, but this is about as bad as it gets, and that ain't bad
As for scanning straight and not slipping two pages through - I make sure I cut the glued edges off with scissors on the pages I've torn apart from the magazine so there isn't a 'thicker' side.
Incidentally, I bought all these Creative Magazines from Erik through the Marketplace a couple years ago.