I don't know how the constant run button is on the pedal. If it's not installed it won't interfere with a remote. You don't need the pedal if your using the remote, I have mine sitting under deck if I need it but it never comes out.With the flag pole, I know what you mean, I have the same shaft and I usually have it way up in shallow water, it can still get pretty shallow but if I need to get even closer I'll take the push pole out and lift the whole trolling motor