Get on You Tube and check out videos on longlining. If you can find some of Russ Bailey's Midwest Crappie shows, he had several on longlining.
You will want to set your boat up with rod holders off the sides and rear. I use HiTeks and have multiple bases mounted throughout my Excel, depending on how many fishermen I have in the boat. Most folks find it much easier to run all the lines off the rear and sides of rear deck when fishing alone.
I wouldn't longline or pull cranks if I had to go back to a foot-control trolling motor. A remote motor like a Terrova or PowerDrive is the only way to go.