Yes, you do have to read your motherboard's manual and check whether there are some limitations imposed by the manufacturer. Also the M2 slots may have shared resources with other PCIe slots. Finally the total number of the available PCIe lanes depends on the CPU you have installed. As you can see you must read that manual.
As for the vertical slot, you can certainly use it but you have to be careful. Usually those slots are used for small SSDs or WiFi cards. It also depends on your PC case and how close that slots is to other cables or components. It may be protected or exposed and it depends on you configuration. If you are careful, you'll have no issue, but you have to plan ahead.
The SSD configuration you'll choose depends entirely on you and your available budget. You can also use an HDD for some "cold" data in order to lower the total SSD capacity, or you can you can also get a SATA 850/860 evo as a second SSD for applications and data. You don't have to get and M2 drive for that purpose. You probably won't notice any difference and it's much more cost effective. You can get an 500GB-1TB 960 pro or evo, as an OS drive and use a SATA 1-2TB 850-860 evo for data. Finally a single tip that I use is to choose a small drive (250-500 GB) for the OS, in order to make my life easier when creating back-up images for that drive. Since you have to frequently back-up the OS drive, it makes your life easier if it's smaller drive than a larger one (1TB+). Good luck.