Scarlet-Tech
It will only make maybe 1-2 degree difference, so kit enough to matter. I currently have my GPUs (all 3) on a 360 and 240 setup. I haven't tested just the 60 vs the addition of the 240, but I know that all 3 cards run very cool. I do believe the 360 supplemented with a thinner 240 would give you better overall performance.

One thing to keep in mind, if the 360 is at the top of the case, make sure to vent the warmest air out first. Have all components run through and then go out the top, so it gets the worst heat out first.

Pump-Gpus-cpu-360-240-res-pump is probably going to be your best bet. This will reduce tubing and give you clean flow.

owcraftsman
IMO if the components in your sig are what we are talking about for a 360 it should be sufficient. 2-970s = very low TDP + 4790k at 4.0 you are probably only pushing 1.2 v core, likely less, you should be able to cool that easily. However if it's your goal to push a higher overclock on any of the above then you will be pushing the limits which would likely result in higher fan speeds and more noise. In there lies the rub, most folks who shift to water cooling are expecting a quieter machine in general. Those who underestimate the TDP will suffer with higher noise to compensate. In regards to loop orientation it makes no difference what order you choose in terms of performance. As the loop temperatures normalize over up time and usage there is no avoiding it's true performance value it's strictly governed by Rad/fan efficiency and loop restrictions/flow rate nothing else matters. The only things that will change its is changing one of those values. For example: different rad, higher static pressure fans or more than one pump which would effect those things.  That said it's wise to be concerned about the choices you make now and it may be helpful to know what case this is going in, which might help us help you better. 

Scarlet-Tech
I can't see signatures, lol.

What case do you have, Peteo? It may be to your advantage that it is on the bottom.