I did finally build over the weekend, aside from a few early software issues everything seems to work. Sadly I had to do a complete wipe to get system stability. First time I've had to do that in years. It will take a while for the bubbles to work their way out of the loop, but even so, temperatures are already excellent.
I tossed a simple 100Mhz/400Mhz overclock on the GPU yesterday 2134Mhz/10,400Mhz result, ran Unreal Tournament (UE4) as a quick test and the GPU tops out at 47C, but I'm not sure that game can actually tax the GPU fully, at least on the maps I played. Still need to do CPU overclocking, but it runs at 4.5Ghz on demand. Ran a quick cinebench and got a decent score.
I'll be updating my signature with the complete build and pictures perhaps tonight, if the overclocking is successful. I also need a sacrificial SATA power connector to add the LEDs to the GPU, and I totally forgot to order my white cable kit. But here is the rough parts list:
https://pcpartpicker.com/list/XNZgCy
As for your questions:
I've trusted ASUS for years so I foresee no issues with your proposed setup. I wanted more features than the Prime series offered, so went with my other regular of Gigabyte. Not too many reviews out for all the motherboards, but that is the price you pay for early adoption.
Programs installed to the SSD will load faster, but not perform any better typically. Keep your favorites on the SSD and leave everything else on the HDD. You can't typically move games around without re-installing, but if you installed everything to the SSD, then moved them, and moved them back when you wanted to play it would work. But you would spend more time doing the transfer than if you just ran the game from the HDD.