Watercooling with AMD Crossfire in BitFenix Prodigy M or DS Cube or analog

I would choose a bigger case because you won't have enough room to fit both gpus and fit a water pump and reservoir in the case. I don't know much about watercooling components but I'm sure other people can help you out with that.

You don't necessarily need a larger case, you just need one better suited to what you are trying to do.
Search for Prodigy M - I've run through some of it's foibles before so I'm really just repeating myself, but it's got quite a lot of issues for even a mid-range build. At high end it's a lot of compromises to get everything working.

If you are unsure about water cooling then I'd avoid it all together - it's very expensive and the priceerformance return is going to be very poor. If you find a mATX case with 5 expansion slots (like a 350D) and a suitable motherboard to support this (off the top of my head I think the G Sniper mATX works for this) then you can leave a slot gap between two cards with conventional air coolers and still keep the cards fairly cool as they have some room to circulate.

There's some other options too.
Alternative cases -
Fractal Design Arc Mini - Pretty small, 4 expansion slots, very conventional but space for radiators
Corsair 350D - Fairly larger for mATX (nearer to ATX) but 5 expansion slots and loads of room for radiators.
Parvum Systems S2.0 - Very suited to watercooling, self assembly, looks not for everyone.
Aerocool DS - Similar to Bifenixes cases but has the motherboard sitting horizontally (like a proper Prodigy) so it's airflow isn't rubbish.
Silverstone SG10 - Three dedicated fans for graphics card cooling (though arguably more suited to reference coolers here), small size, similar cubic form factor.

Alternative graphics cards -
If you are going to spend a load of money buying full water cooling and water blocks for graphics cards, the cost saving on getting GTX780s over R9 290s really isn't that significant. By comparison, the GTX780s have a very solid reference cooler you can stack up reasonably well in smaller spaces (especially if you have direct fan support like on the SG10).

Go single graphics card -
Dunno if you've considered this, but do you actually need dual R9 290s? If your running a single display, even if it's 1440P, there's a case for it being a waste of money. If you want a smaller, watercooling build, then there's much more flexibility if you only have the one graphics card.
ITX Bitfenix Prodigy - Much better airflow, layout and radiator support than the "M" version. Works fine on air, but has good water cooling options.
Corsair 250D - vaguely similar layout to the Prodigy but less suited to air - more of a closed loop cooler system.
EVGA Hadron Hydro - Very small, unusual looks, packs a lot of stuff in, but limited options.
Ncase M1 - Good luck getting one, very cool though.
Compact Splash - Great name kinda explains everything.
Caselabs Mercury S3 - Expensive but loads of options/configurations.


For general watercooling advice if you do go down that route, have a look at the watercooling sticky. If it seems intimidating, it's kinda because it is. What sort of radiators you will need depends on a bunch of factors, all of which are addressed - things like fan speed/noise, levels of overclocking etc.

Man, that would be a challenge.
TBH, I dont see any way it can be done while still keeping the case aesthetic (so externally mounting WC'ing gear) or its portability (a dock kind of setup).

Dual cards in that case is already a tight fit, at best you might get a 200m rad at the bottom and a pump (depending on the size of your PSU and no 5.25" bay). Your definitely going to need more than 200mm of rad space, so anticipate a external rad (240 or 360mm) on top and a reservoir (you could pretty that up pretty well actually).
You could limit this back to a single card, getting an R9 295X2 will give you a lot more room to work with (internal mounted 240mm rad for instance).

However.

If this is your first computer build, I recommend not even going near custom water. Its already hard enough that you picked this case, adding water to the mix just makes it so much more complicated. Whenever something goes wrong with my rig I dread having to troubleshoot it, because if its something that requires me to pull hardware out or I need to breadboard, there goes your day. Water-cooling pretty much anchors your hardware to the case, and it requires a lot of work to extract it.
My opinion, dont even consider water on your first build.