I agree with the "real" bass players who say marks are a crutch, but for those of us who want to import our BG knowledge (and in my case, jazz guitar chord theory) to the DB, it does take the guesswork out -- but certainly it doesn't absolve you of the responsibility to constantly listen for intonation -- that is a must.
What I like about setting permanent marks is that it gives you a constant reference -- so, for example, if your tuner tells you that the dot you made for an A (i.e. the imaginary fifth "fret) is out of tune, then you know you're bridge is out of place (or else the neck is buggered). HOWEVER, I must re-iterate that before you make any marks permanent, you must have your instrument set up (including, most obviously, bridge placement) before you make the indentations; once you're set up, then you can proceed to find the centre of each dot using the tuner -- bear in mind again, tho', that your finger is somewhat wider than the dot, so to find the true centre for the dot placement, you might think about stopping the string using a thin wood dowel for greater accuracy. And again -- before you make any indentations -- double (or triple) check the spots for tone accuracy, and then check em again.
gk