Try this setup:

• Bottom - Two intake fans
• Side - Two intake fans
• Rear - One exhaust fan
• Top - One exhaust fan

Tl;dr:

With your current setup, aim for slight positive pressure by setting your exhaust fans at a higher speed than the four intake fans (e.g., exhaust - 900 rpm, intake - 800 rpm). This may give you the best balance in noise, cooling, and airflow.

Advantages of this new setup:

• Reduces noise since you can set all fans to a comfortable speed
• Optimises airflow to achieve either neutral pressure (ideal) or slightly higher positive pressure to reduce dust
• Exhausts hot air at a rate that does not allow the air in the case to heat up

Explanation:

Mount the top exhaust fan as far left as possible (over the top left corner of the motherboard). The ideal airflow pattern in any system, not just computers, is to get air in at the same rate as you get air out. The ideal is neutral airflow where there is no pressure buildup in a case - air leaves as quickly as it comes in. The next preferable pattern is positive pressure - simply because it helps to reduce dust - where a slightly higher volume of air is brought in than exhausted.

With your current setup, you have too much positive pressure, which is very bad for cooling. You’re introducing an unnecessary volume of air that’s bouncing around in that case. The reason your temps get worse is because, while in theory it sounds like shoving more air into the case would be great for cooling, but the problem is that air isn’t leaving the case fast enough! So what happens? You’re shoving so much air into that case at such a fast rate, and it has nowhere to go! Sure you’ve got one exhaust fan that’s trying to pull some air out of the case, and I guess you have some breathing holes at the top, but there’s nothing up there to direct that air, so air will partially get pushed out of there slowly, but it also is forced everywhere in the computer and gets pushed in all the cracks and crevices in that case (e.g., between the glass and the case). In other words - the air in the case is somewhat trapped and it actually gets hotter since it has nowhere to go! This is why your temps are worse by adding those three intake fans. You need to get the hot air out at the same rate it is coming in, and exhaust fans will do that for you.

Key: The air coming in should leave the case at the same rate. A compromise, where the only benefit is to help reduce dust, is to have the air leave the case at a slightly lower rate than it came in.

You only need one rear and one exhaust fan. You’ll see other builds with three fans mounted on the top, but that is extremely wasteful and misguided. Those extra fans end up exhausting cool intake air before it even has a chance to blow over the motherboard.

Set your exhaust fans slightly higher than the speed of your four intake fans to help balance them out. It is two exhaust vs four intake, so you can try something like this: intakes at 800 rpm, exhaust at 900 rpm. Of course, set up appropriate fan curves when you’re introducing load to the CPU and GPU so they ramp up appropriately.

As for optimization, your definition of noise may be different from others. Introduce sustained load to your PC, and then while you have that load, play around with your fan settings to figure out what you’re comfortable with and set the fan curves appropriately so that they gradually ramp and stay at consistent speeds.