I'm on a bit of a crusade concerning selenium toner. First, I believe it is unnecessary to discard it. I mix my toning solution with water (not a wash aid) and never discard it, but replenish it with concentrate from the bottle when toning times get too long (it just takes a little to bring the toner back to life). The toner is filtered through coffee filters before and after each toning session to remove any precipitate. This prevents one from dumping heavy metals into the environment and is more economical as well. I find it ecologically irresponsible to toss active toner.
Second, I have always printed in two stages, giving my fiber-base prints only the first fix during the actual printing session. I then collect a larger batch of prints to tone and do the toning all at once. My procedure is: pre-soak, second fix and then directly to the toner without any wash or intermediate rinse. This saves time and I have never had a stained print. Pull the print when the tone is right. The other posters are right in recommending you keep a wet, untoned print handy for comparison. Also, I often print a bit less dense, counting on the toning to deepen the blacks to acceptable level. Sometimes, if you are not careful, the toning can unacceptably darken a print. I like quite a bit of tone change and use dilutions from 1:9 to 1:20 depending on paper type.
Hope this helps a bit. ;^D)