My fan setup
I have 2*140mm fans on my window as an intake.
I was concerned about dust build up inside the case, and was looking into filters - but decided against it after monitoring the dust build-up for a few weeks.
The fans will only ramp up as the GPU gets too hot - and as such the ventilation will be used to expel air as the case had positive pressure.
Sure, once they turn on they'll be bringing dust into the system. However, they're only on while under intense load and the benefits of this outweigh the minor inconvenience of dusting the system.
This is in my case, and I'm sure yours will differ but I have had no problems what so ever with dust coming in there as the window is quite far from the floor.
All my other intakes are filtered and PSU is independent from the case airflow. It may also help that I'm running a very easily maintainable Corsair c70 where everything is aircooled and very easily removable. I plan to clean my system every 4-6 months.
If I were you (and again, if the situation permits) I'd have the top and rear as exhaust, with all others as intakes.
The top of the system is most notorious for dust build-up - especially as an intake - so prioritize it as an exhaust.
If you're too concerned about dust build-up there's not much you can do except re-arrange your intakes or filter the window fans, but again, used appropriately they will only be a problem under extreme load.

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