Always after -- like you thought, the spot tone will tend to wash off -- plus selenium toner will react with the silver on the paper and cause it it to change color (depending on the paper, developer, etc), but the spot toner will not change color and will no longer match.
I standardized my process (including the toning) so that I achieved the same print color at the end of the process. That meant I could work up a set formula for my spot tone mix to always match the print color. Actually I had two print colors -- a neutral black (Ilford Gallerie/Dektol) which toned well with Spot Tone #3, and a warm tone (Agfa Potriga Rapid/Dektol) which toned with a combo of 5 drops #3 and one drop "B"(or something like that -- it has been awhile!).
Vaughn