Yes- while they are beneficial to take all the time, while taking abx is the most beneficial time to take them, since abx tend to kill off both bad AND good flora in our system.
I am not sure if time of day that it's taken is significant or not. Maybe someone else will have input there. I give Emily a multi-strain formula twice a day; one that's coated to better survive the stomach environment to get to where it needs to be in the intestine. She takes it all the time, whether on abx or not.