Homebrew PCBs

I think you can also export to a standard image file as opposed to 
printing. This should allow you to manipulate and paste it in whatever 
program you want. Windows screen capture to jpg (print screen button?) 
may work too, but either way I'd check the dimensions in your graphics 
app. If the resolution is decent, it should at least save you whatever 
difference the extra scan steps might make.

I normally do the Eagle "page" technique too. I usually move things 
from top to center to bottom, actually slicing the paper into thirds. 
With my regular photo paper, I haven't had any trouble feeding the 3.
66" sheets. For the really small boards, that way still sucks, and on 
occasion I have moved the horizontal alignment as well, just letting 
the finished prints run through more than once to get two or three per 
row (not sure what the extra heat does to the toner).

-George