I believe these boats still come with a 5-pin connector. The 5th pin is a reverse signal to the surge brake actuator to disable the brakes when you try to reverse. You can get away without it but you will need to lock out the surge brakes with a little key so make sure they give you that. You will also probably need some kind of adapter so that you can still connect the trailer lights.
If you wanted to install a 5-pin on your vehicle (which I would do), I believe you can just splice off of the reverse lights and run that to the new connector. Here are the different wire configurations. My trailer came with the flat 5-pin, but that was 4 years ago so I would check with the dealer what will be on your trailer.
Trailer connectors in North America - Wikipedia
You can use either the shipping cover or the mooring cover for towing. I like the mooring cover better because it hugs the hull a little better, but if it's rainy, I like to use the shipping cover because it's easier to clean. Either will handle the wind though. My preference was to drive without the support poles, but some people prefer them in.
I sincerely hope you don't have any tire issues, but I always keep a tire iron in my truck. The lugs were a different size than my Jeep or my pickup so the vehicle wrench would do me no good. I would plan on getting a spare right away if you didn't order one with your boat.
Congrats on the new boat and don't be discouraged if you struggle with it a little at first. We all did. I don't regret a minute of it!