Ultimately how you set up your boat depends on you and how you want to fish the seaway. There is no best design or layout.
I do recommend a floor of some description as being able to stand up and move around without falling over helps alot but is not absolutely necessary.
Good fixed trolling rod holders are recommended if you want to do some trolling, and by good I don’t mean those plastic rotatable ones you buy in the boat stores(they will snap if a big enough fish hits the lure).
I personally don’t like vertical rod holders to hold spare rods as they will get in the way when you want to cast at a school of surface feeding fish, I use horizontal rod holders and it enables me to use a 360 degree casting area. The more accurate your casting the more fish you will catch.
Another thing I recommend if you intend on fishing the outer ends of the walls(12ft tinnies can do this easily..with care) is a water separating fuel filter, it will remove any chance of the motor cutting out due to dirty fuel, and believe me thats the last thing you want when the wind is coming from the south.
Most of the guys who use 12ft tinnies in the seaway use 15hp outboards to give them some top end speed to chase surface feeders, but 6hp is fine if you just want to fish plastics on the bottom or fish the pipeline.
I don’t use an electric as it slows down your reaction time, but sometimes they can be useful if the fish are holding in one area.
Before you start messing around with your boat try a few trips in the seaway without changing anything, if you haven’t fished it before it will take a while before you get the confidence to try every aspect and along the way you can make modifications to your boat if something needs improving. I’m still making changes to my boat 7 years after I bought it.