Side by side, long side horizontally. I move my chair and keyboard around a bit depending on my mood, but typically one is directly in front of me, and the other is to my right.
The one directly in front of me is usually for the "primary task", e.g. my editor if I'm programming, usually with multiple files displayed side by side. Sometimes also a single documentation browser window (other times just more editing panes). The one to the right for all the supporting stuff, (more) documentation, stack overflow, github, terminals running scripts that rebuild stuff whenever it changes, etc.
The one directly in front of me is usually for the "primary task", e.g. my editor if I'm programming, usually with multiple files displayed side by side. Sometimes also a single documentation browser window (other times just more editing panes). The one to the right for all the supporting stuff, (more) documentation, stack overflow, github, terminals running scripts that rebuild stuff whenever it changes, etc.