I would just run it side/front and bottom as intake then top and rear as exhaust. this will give you slight positive pressure which will basically make the only dust entering the case at the intake fans, which is where you hopefully have your dust filters.

It will also give the best air flow for cooling you other components. While I know its a water cooled build the rest of the components that don't have a block on them still want, and are designed to have, air flowing over them to help keep them at operating temp and is best for longevity. Especially in a rendering rig, that will sit there saturating in heat for hours, I would want to get the air in and out as quickly as possible and moving over the components to help them last a long time :)

That said, having it on the floor is going to be the dustiest place you can put it. It's just where everything settles and tends to get sucked in. My buddies rendering rig is wall mounted, runs basically 24/7, has a slight positive pressure, and rarely gets opened for cleaning because it just doesn't get dusty! A big part of that is the wall mounting...any chance you can get it up on a shelf or something? That would help a lot