Okay, so that DIY was super helpful. Here is what I discovered. My intuition was correct, those lines were meant to connect to those two ports on the engine. The reason why the shorter one in the first picture wouldn't connect was because it was the wrong tube. The tube that connected to the bottom port was too long, when I tried to connect it where it was supposed to go, it kinked up the line, and that shorter line barely reached that top port. I had to disconnect the third tube a little deeper done, and lucky me, coolant started pouring everywhere, but I was ready with the shorter tube I pulled off, and stuck it on there real quick. It connected perfectly. The hardest part was pulling all of the tubes off, they were super stubborn, and that third tube down a little deeper was the worst one to get off. My coolant was low, and my reservoir was, as far as I could tell, empty. I guess because everything wasn't connected correctly. By any chance, is there a possibility that I can hold the body shop liable for not having everything hooked up correctly? That third line was connect in the wrong place, so I don't even know what my coolant was being dumped into, and of course those first two tubes that I posted weren't connected to anything, and that bottom port on the engine was where that third coolant line connected to. Fortunately, I had some Honda coolant left-over from when I did my coolant flush, so I was able to fill up my reservoir, and top off the radiator. My main concern is what damage may have been done to the engine. I'm guessing I should still take it to a mechanic? I fixed everything and have it all connected properly, but I am worried about what effect this may have had on my engine. Thank you again for the super helpful response. You're a lifesaver.