I don't really know why you would use a PCIe SSD when it's going to cause you problems. Standard SATA SSDs solve the problem instantly.
The other stuff is really up to you. There should be no major issues finding a motherboard which will support a Wifi card, soundcard and 2slot graphics card, though a lot of mATX boards will have at least one legacy PCI slot (often at the bottom) which you can use for a Wifi card, though not the one you listed.
Now, you haven't listed your other preferences on components (or budget) so I'm kinda playing guesswork here. I'll assume that A) you are going Intel, either i5 or i7, and B) you are going with the most modern socket 1150 (4000-series Intel CPUs).
Few motherboards which will fit sound card and network card you listed plus a 2slot graphics card -
ASRock Z87Extreme4M
Asus H81M-PLUS, H87M-E, H87M-Pro, Z87M-PLUS, GRYPHON Z87, Maximus VI GENE
Like I say, if you change the Wifi card to PCI, there are loads, but you do need to be careful here. Which chipset you need will depend on the rest of your specs/needs really.
The mATX Prodigy will cause you a lot of issues, some minor, some more annoying. There is quite a lot of "you can't fit X if you have Y type of scenarios which can be problematic. I'd suggest sticking with a popular compact tower like an Arc Mini or Corsair 350D, but once you hit those sort of dimensions you do have to ask yourself whether it's worth bothering with mATX at all (the footprint is going to be very similar after all). If you really want a mATX Prodigy, then have a look at the Aerocool Dead Silence, it's more like a standard Prodigy in layout than a Prodigy-M and looks fairly similar.