I think I can help with a few things, but this won't get all of them.
Rear Fan
Mechanically installing the fan, and plugging it into the mobo fan header, is straightforward. It's the fan header configuration you are concerned about. It's done in BIOS Setup, so let's review that. You have the mobo manual, you say. Start on p. 3-1. To get into BIOS Setup you push the "Del" button immediately after pushing the on/off front button. I find it is not enough to push and release. I always push and h9old it in until the opening screen of BIOS Setup shows - see p.3-2. It may come up in EZ Mode, or in Advanced Mode (p. 3-3), depending on how an item has been set before. In either case, after making adjustments you will come back to this screen. Then you click on the upper right "EXIT" item to get to the Exit Screen (p. 3-48.).
From EZ Mode, click on that upper right item to get to Advanced Mode4. Then c;lick on the Monitor tab at the top - see p.3-40. Your mobo has four CHA_FAN headers, so scroll down to click on the line For "Chassis n Q-Fan Control", where "n" is the particular header your rear fan uses, and ensure that this is enabled (p.3-42). Next you can adjust the Low Speed Limit for that fan. This is just the low speed limit that will trigger a warning on your screen that this fan has stopped or failed, so set this to whatever your fan's specs suggest is its lowest reliable speed, or maybe a bit higher if necessary. Next item is the Chassis Fan n Profile, and this is the setting of what will be the fan min speed at a certain low temperature on the mobo, and of the max speed at some high temp. I suggest you use the Standard setting (a generally-good pre-set Profile) for this at first. IF you find that the fan is running too slow for your liking, OR that the fan actually stops because the mobo temp is quite low already, you can come back here and change to the Manual Profile Option. If you do that, you will find your settings you can make for that (outlined on that page) and set the fan's minimum speed somewhat higher than "normal" when the measured temp is low. When you have made your fan settings, use Esc to return to the Monitor Menu, then Exit at upper right to Advanced Menu, then Exit again to get to the Exit Menu (p. 3-48). There click on Save Changes and Reset and the machine will reboot.
Video Cards
I suspect that your system is fitted with two video cards from the same GPU family (although different models from different makers) that are actually "joined" by a connecting strip across their top edges into a 2-card NVIDIA SLI configuration. The two work together, and only ONE of them furnishes the output from that "team" of cards. I expect that "boss" is the MSI Gforce 980 one with two fans (one of them with red trim). That one, by the way, has a fan control system that runs the second fan only when it is needed because the card is hot from working hard - otherwise it stays shut off. You have a CD of utilities for the 3-fan Palit 780 model, and using it you may be able to see and adjust IF you need to) the fan system on it. For the MSI 980 card you can find help here
https://ca.msi.com/Graphics-Card/GTX-980-GAMING-4G/Overview
Click on the Support item at top and you can find the Quick Guide and Utilities for it to download. Regarding display modes etc., I expect BOTH cards will be adjusted using the video driver software you have, because they are treated as one video system.
After you get these settled, we can discuss how to clean up the rest of your issues.