ALWAYS go from the nut, not from fret to fret. If your off by say a thirty second each time and go from fret to fret by the time you get to say 16 frets the total error could well be a half inch off. It IS a good idea to check the fret to fret spacing though jus to be sure.
Personally I like to work metric in laying out frets if I happen to be doing something thats not using what I consider my normal VSL. Less thinking involved.
Just tape down a good 2 foot steel rule with masking tape so it wont move then all you gotta do is put your marks at the right spot. None of that line counting stuff like lets see 3/32, etc.
For the VSLs I normally work with I created some paper templates with autocad I simply stick down with a glue stick then just cut on the lines. These are fully chromatic with the diationic frets marked on them. If I want diationic ( dulcimer) fretting, i sinply cut the diationic marked one. For chromatic, I get them all. The spacing values came from my copy of Fretcal and its checked against several others. When youre through slicing up the fretboard just dampen the paper and it comes right off and witha good wipe of a damp rag, the rest of the glue is gone too.