Mine doesn't get in the way. I use a TightLoc system where the only thing bolted to the boat is the small channel that the stand slides into. I can adjust it right and left to make room for the trolling motor. I would place my trolling motor in the stowed postion and then put the rod holder where I thought it would not get in the way. Then have someone deploy the trolling motor to insure it will clear the rod holder. May have to adjust it a few times before you get it where you want it. Once you do, mark, drill, and mount.
Hope this helps.
The Hound