Changing a motherboard is as hard as you make it out be, and your chances of ruining something are inversely proportional to how careful you are. Since this is your first time, I'll give you a few pointers to get you started.
1. Clear a nice big, flat workspace.
2. Make sure that you have adequate lighting
3. Also have a nice flashlight handy. LED ones work great.
4. To swap the motherboard you will have to remove and replace the CPU. To remove and replace the CPU you will have to remove and replace the heat sink assembly. To remove and replace the heat sink assembly you will have to remove and replace the thermal paste. To remove and replace the thermal paste you will need some solvents and cleaning material.
My personal favorite is electronic contact cleaner which can be purchased in compressed cans. This stuff just melts thermal paste away in seconds. However, Isopropyl alcohol works just fine; you can use Q-tips to scrub the paste away.
You will also need new thermal paste to replace the old stuff. I recommend Arctic Silver 5, but MX4 has also been recommended around here.
5. Be careful disassembling and reassembling components. Treat your PC like a patient on an operating table. Use the appropriate tools to remove each component (usually just a Phillips screwdriver) and set them aside gently. Remove all the cables that you possibly can or lay them such that they are away from the center of the case; if you don't, they will just get in the way. When you get down to the motherboard, there will be 9 screws that you have to remove. Remove these and then gently slide the motherboard out.
6. Take the opportunity to clean your case out. Remove your fans (including the one on your heat sink) one by one and scrub them gently in hot soapy water. Finally, lubricate them with WD-40 and spin them a bit to let the lubricant work its way in. Reassemble them as you see fit.
7. Your new motherboard will come with a new IO shield. Pop the old one out and replace it with the new one.
8. Repeat (5) in reverse. Insert the new motherboard and seat it properly against the new IO shield. All 9 ATX holes should lineup with the standoffs on the case. Once they line up, you can screw them in with the same 9 screws that you removed from the old motherboard.
Insert the freshly cleaned CPU. Make sure that it's seated properly and close the latch. Don't force it; if it's seated incorrectly, you'll damage something.
Apply a small dab of thermal paste to the center of the CPU. When I say small I mean small, about half a centimeter in diameter and about 2-3 millimeters high. The heatsink and CPU will be pressed into contact and the paste will spread out. It's amazing how little is actually needed.
Reseat the heatsink and attach the bolts that hold it in place (if it's a stock heatsink, they may be plastic plugs). Do not screw the bolts down one at a time, alternate them bit by bit until they're all reasonably tight.
Insert the memory and make sure that it snaps into place.
Insert the graphics cards and make sure that they snap into place. Use the appropriate screws to secure them to the case as well.
Insert the appropriate power cables to the motherboard and PSUs. The motherboard will have a 24 pin connector and either a 4 pin connector or an 8 pin connector. The GPUs will have some combination of 6 and 8 pin connectors. The 8 pin connector for the motherboard (if present) looks nearly identical to the 8 pin connector for the GPU but it is keyed differently and will not fit.
Run the sata cables from your hard disks to the appropriate ports on the motherboard. Some motherboards contain a variety of SATA-III and SATA-II ports from the chipset, as well as ports connected to an add-in controller. In general you will want to use the SATA-III ports on the chipset for SSDs, and the add-in controllers as a last-resort. Consult your manual to see which is which.
Route and connect the front panel connectors. Normally this would be done before inserting the GPU, but since you have two GPUs it should be done last. Consult your motherboard manual to determine where to connect them. Use a pair of needle-nose pliers and that aforementioned flashlight to make your life a lot easier.
9. While your case is still on the operating table, plug it in and fire it up. If all goes well, it should POST.