Hi..The mobo sure fits in the case perfectly, both stick to the ATX standard. But I have to ask you do you intend to have SLI or crossfire setup? If yes, I may recommend something else to you.
The 6 fans in the antec case connect directly to the PSU (power supply unit) and since they come with a knob or switch to control the rpm, you can optimize airflow/ noise to your liking and you won't need to connect them to the Mobo, .
Yes... The motherboard will fit into the Antec 1200 (Great case & motherboard selection ).
Outside of the form factor, as you mentioned, you need to look at expansion slots on the case and take into account your video card size & or SLI/Crossfire setup plans in the total picture of case/motherboard compatiblity.
I have all my case fans plugged into my molex connectors on my power supply. Also, I would look at getting an 8pin ATX extension so you can route the cable behind your motherboard.
edit: Note to myself... Remember to refresh page you left open for a while before posting to make sure the same answer hasn't already been given