First I set the spacing of the two outermost strings so that I achieve the desired string-line relative to the edge of the fingerboard. Then I use the stewmac nut spacing tool to do the rest. Foolproof.
Let's say it's a Martin with a 1 7/8" nut width. My spacing between unwounds and unwounds/wounds is 3/32". If both strings in a pair are wound I'll increase that spacing to about 4/32"