I have a somewhat complex layout that I want to make constraints for. 
Top three all need to be equidistant from each other and equal widths and heights. Bottom three need to be equal width and heights, and also equidistant from each other.
How come Xcode doesn't have an equidistant margin option? I can't create a specific margin constraint because it wont look correct on smaller devices. Nothing I do seems to create acceptable constraints.
Thanks!
For top three you need to create 5 additional views, place them between this three views and set that they should have the same width. One of them should have some constant width(than all other will get this width as well). Than bind them all by connecting leading and trealing constraints between them. Next thing to do, is to set your views width and height. Margin that you need will be that five views that you placed before between them.
The same thing you can do with your other views, just adding some views to make them as a margins.
Is it what you was searching for? If not Pls describe your problem and I will try to solve it.
As @Dan said, UIStackView is your friend. Put the top three in a horizontal stack view and the bottom three in a vertical one. Your other alternatives are to fiddle with the Multiplier on individual constraints, i.e. 0.0 0.333, 0.667. That would require a lot of work. One other choice, if you're willing to wait to use this in Xcode 8, is that Apple has reinstated the old springs and struts style of pre-Autolayout in Xcode 8, and allows you to use that as an alternative, and/or mixed in with auto layout in Xcode 8. Try the UIStackview first, though, it's the path of least resistance.
UIStackView