need help deciding motherboard for new build

To clear up a possible point of confusion, mainstream motherboards are primarily sold in three categories - ATX, mATX (micro ATX) and ITX. There are other types, and some slightly variations in size amongst them, but essentially, that's your selection.

Personally, I don't think the Prodigy M is a great case. I'm a pretty big supporter of the ITX variant, despite it's flaws, but for me the Prodigy M only adds to the negatives.

The reason you will find Wifi on most high end ITX boards but not mATX/ATX boards is because there is no room to add a Wifi card.
You would normally chose a mATX board over an ITX one due to cost, limited expansion potential (in terms of PCIe slots and ram) or interest in running SLI/Xfire. As a generalisation, larger motherboards are better performance parts due to the extra space available, and easier support for large coolers. That said, the Z87I and Impact are incredibly good performers, and support more or less any CPU cooler (though check in advance) but they don't represent good value when compared alongside their larger cousins.

If you can afford the slightly eye watering price, then the Impact is very impressive. I'm not sure what the sound issues are, pretty much every review I've seen says it's amazing but expensive. A lot of the price difference over the Z87I is paying for that little sound card.

If you do go with ITX and the Prodigy case, your cooler options are pretty enormous. It supports 240mm radiators in two places, but this completely removes the ODD bay which if you already have a DVD drive bought, won't appeal much.
120/140mm rads are absolutely fine though. I use a basic Antec Kuhler 620 myself and there is loads of room.
Alternatively, and perhaps the best way, is to go for air cooling. Something like a Hyper 212 Evo will do you fine for a basic overclock, though if you really want to push the boat out, a Noctua NH-D14 or Phanteks PH-tc14 is top end performance. If you do go down the expensive route, it'd be worth upgrading at least the front fan to a 200/230mm to increase airflow around the drive bays.