Personally, I would go with your suggestion of installing the hybrid rads in 1 and 4. The Air 540 case has whopping big holes in the bottom of it, so you ideally want a slight positive pressure in the case to keep dust out (i.e. more air coming in to the case than coming out). Do remember however that an unrestricted fan will move more air than a fan mounted to a radiator, even one designed for static pressure. Also bear in mind that the 2 GPU's have attached blowers that exhaust air out of the case as well, albeit only a relatively small amount since the speeds are slow on the hybrids.
Of course for most people this is probably not that important, but I am overconscientious when it comes to temperatures.
EDIT: Forgot to mention that if your radiators are mounted vertically (which they would be in positions 1 and 4), the hoses should be at the bottom. This means that any air in the system will sit at the top of the radiator (the highest point) and no longer be drawn in to the pump, which can create an annoying gurgling sound (and even increased temperatures in extreme cases). Some people have issues with this, some don't, so it is worth installing this way around if you have the space just to avoid potential issues entirely.
EDIT EDIT: Also remember that you are right that you would want the radiator installed in position 1 to be set up as intake, but remember that this will mean that ~30% of the air coming in to the case will then be effectively preheated, so you may need to increase the other intake fan speeds to maintain a low temperature inside your case, and you *may* find a very slight increase in your cpu temps, although this should be relatively marginal. You might also find that the hybrid installed in to position 4 will run at a slightly higher temp as well, for the same reason.
Installing a radiator as an intake is not ideal, but in your case, you don't have much of an alternative, unless you want to either buy a new case, or go full custom, which kind of defeats the point in buying the hybrids. I doubt you'll find the temps that terrible to be honest, but bear in mind what I said earlier about my obsession with temperatures, lol.
post edited by Makalaure - 2015/11/26 23:37:51