step/dir setup

["Ronald J Heaps/RJH/CC01/INEEL/US" <RJH-at-inel.gov>]

I finally have things appearing to work in emc (green lights and all). But
I think my pinouts are wrong.
>From the dos program "turbocnc" I figure these are my settings.
Motor     step dir
X    2    3
Y    4    5
Z    6    7

When I go to Linux things don't work. Looking around it seems the default
emc pinout is.
Motor     step dir
X    3    2
Y    5    4
Z    7    6

How do I go about changing the pin assignments for my parallel port?