Just pull the hose out and throw it away. The top hole is factory. Then just get another plug for the lower front of the bed. Plus pull off the tonneau side rails. Sounds as if you didn't get the actual tonneau in the sale.

 

I guess for wiring or what have you
Thanks everyone for ideas

 

I will check if the hose fit where you pointed in the picture, that would be the best place to drain the water when I have the cover on. Thanks

 

You were right, it fits perfect on that spot. I was wondering why I have water on rainy days when I have the cover on. This should fix the problem. Thanks again

 

Where does the other end of the hose go? Perhaps a to a vent, trans ect for off roading in water, or it came off the circled item? A drain for it.

 

The top of the hose came off the area with the red circle, the bottom goes outside in between the cab and the bed( exactly in the center of the picture). I'll probably need to put a cap on the uncover hole where I had the hose before I knew it was on the wrong place(at least in my case to drain the water from the rails when the cover is on).