There are 2 major resources for mapping your course.

www.missouririverwatertrail.com has excellent maps and information.

Also, the old Lewis and Clark maps the Corps of Engineers put out a few years back have been archived on our forum here: http://www.rivermiles.com/forum/YaBB.pl?num=1357573158 There are 8 sheets in PDF format. You can print them off. They work well for paddler AND ground crew.