We trailer a lot - last season over 5000 miles. I always use the cover with the poles. Our boat is stored indoors when not on the water or being trailered, so the cover does not get a lot of stress from sun or winter, etc., only during actual towing.
On our former boat, we did use cushions in the bow to hold the cover up, and used pipe insulation on the windshield, but that windshield had sharper edges, and the bow pole was not as stable. With the Yamaha, we have only relied on the poles and cover. Some people get concerned about etching of the windshield- I did experience that on our last boat (over 24 years of ownership), but I opt to use a cover to keep the boat protected and minimize wind resistance. No perfect answer on that.
I tried using the brackets and folding the tower, but the cover does not fit properly with the tower down (at least on our boat) and the shipping brackets in place, so I generally tow with the tower up. Catches lots of insects, so we do keep cleaner handy.
I would make sure your trailer and tow vehicle are optimized for best towing efficiency. Most important is towing a level trailer. Another help is to check your tongue weight and adjust as needed. Many on this forum have reported heavy tongue weight. Ours was about 175 lbs heavy. This adds stress to the tow vehicle unnecessarily. If you have a Shoreland'r, refer to their manual or web. They generally recommend 5-7% of the total weight. If it needs adjustment, many on this forum move the bow support and slide the boat as needed. That works, But is not the way Shoreland'r recommends adjusting tongue weight. They say to have the axle assembly moved to adjust this. The entire axle assembly is designed to be moved along the trailer rails. It does require jacking the entire trailer up though. You will also find several threads about tires on this forum. Yamaha generally supplies the trailers with bias ply tires. For long highway towing, you would improve efficiency with radials.
You've got some great boating lakes in TN! Have fun!