It is personal preference whether you use the "basket/ mesh thing" on your pontoon.
I tried mine a few times and took it off after finding it gets in the way. There are a few advantages to using it.
If you change spools on your reel often or have a tendency to drop things in water (camera, forceps, flies, nippers, sandwich, granola bars, etc) it can be handy.
Good luck with the new pontoon! They're awesome!
stan