How to draw diagrams is largely artistic choice.
The one mathematically based rule I can think of is that pullbacks should always be parallelograms.
The point is that pullbacks capture substitution, change of base, etc., so that they translate onone part of a diagram into another.
The word translate there has a deliberately double meaning: the linguistic one and (so long as you use parallelograms) the geometrical one.
On second thoughts, this argument applies to naturality squares too.
Other than that, I try always to draw adjunctions vertically, so that the left adjoint is on the left and the right on the right.
OK, so maybe there is more than one rule.
Happy commuting!
