When I try to print from the stack bypass tray it takes the paper from cassette x or tells me to load paper in cassette x.

For most of the Canon B&W networked printers the stack bypass tray default setting is free size (or the like).  The print board must know the size of the paper in the tray before it can use it.  This is a customer feature and is easy to turn on. (RTFM)

For the newer iR machines. (updated Nov 4, 2002)
iR2200-3300(i)/5000-6000(i)/7200-105
The default setting rock.  When you add paper it asks what size.  Don't pick free size.  If you will always be using the same size you can set that in Additional functions-common settings.

For the IC22x0

The arrow keys can be found under the three speed dial panels.
There are four triangles, each pointing in a different direction.

Press Data Registration (set)
arrow to printer settings (set)
arrow to name stack size (set)
select on (set)
select paper size you are going to use in the stack bypass (set)
make your way back to the default screen your done.  (reset)
 
 

For the GP200E\F, iR210, 330, 400

Press Additional Functions
custom common settings
arrow down 2x to screen 3
select Stack bypass size entry
select on (ok)
make your way back to the default screen.  (done, done)
put your paper in the bypass tray and select the correct size from the display (don't select free size)