Diference between Certificates in "Login" and "System" for XCode
The System keychain is for System wide items. So if you were to have an identity for you laptop, that would be in your System keychain. Every user has access to it as well, so it's a good place for things like SSL certificates. It also takes admin credentials modify it.
On the flip side, you are the only person who can access your login keychain. It's actually locked with your account password. This is where your Apple Developer certificates should go. They are specific to you and identify a person, not a machine. Another big plus is that applications can request access to it without having admin credentials.