I normally fish two brakes and I know when you set them up you should always have the brake pins set up opposite each other but what if I want to use 3 brakes how do I go about setting that up?

Every other one gives you three equally spaced.

If you need the third brake, turn it on. Any unbalance it causes won't be noticed

I put two on last year when I bought the reel and have not changed it.  Actually, every reel I have has two brakes on.

It is just a myth that said if brake blocks not on opposite alignment, the spool might vibrate when cast.
Is it true? Some what yes but in rare case. The vibration will cause some noise and a little distance. The shimano reels have a tight tolerance, the vibration shouldn’t be any noticeable or uneven brake blocks.

For your SLX with 6 brake blocks, you can do 2 across, 3 every other, or 4X. 

I’m waiting for those shimano expert to come out and said that is not true lol.