I learned early on that when working on any scale whatsoever, one ought not to trust the timber. I do all of my work by snap line, though not necessarily square rule.
I work off of reference lines, because even if a timber comes out of a top quality mill and is minutely adjusted with a plane, wood is organic and always moving. So what's square today might not be so square tomorrow.
The most important thing to wrap your head around is that measurements won't be coming off of a timber's edge, but off of a reference line.
I like large-scale layouts, akin to what you would need to scribe a frame. Because I can use these to derive all theoretical measurements -measure from reference line to reference line, with no timbers present, then I can figure out empirically what I need. If I do this, I can figure out brace lengths and complex framing members without complicated math (just simple addition and subtraction)
The best part of this is that when working off of reference lines BEFORE laying out the timbers, I can make cut lists that will yield consistent framing members that, once cut to these specifications, can only possibly go together square and perfect.