Here are some tips from Lowrance. The ferrite blocks they mention are available at Radio Shack.
If you get lines on the screen or the unit reads erratically when the trolling motor is running, this could indicate trolling motor interference.
Trolling motor should run off of a separate power source than the unit. Use 2 different power sources if possible.
Make sure cables are on different sides of the boat.
When using skimmer transducer on motor, use a piece of rubber under the transducer.
Use ferrite blocks, one on the transducer cable, and one on power cable. Make sure to get the ferrite blocks as close as possible to the unit.
Ground the foot-control pin on the trolling motor to the negative terminal of the trolling motor battery.
Fair Winds and Following Seas
Bill H. PTC USN Ret
Chesapeake, Va