If a 2 y/o has a low Stamina rating I will give them two 5f races and a 6f race.
Keep an eye on the stamina bar throughout the season as this can start to move and I use this as an indication that the horse is ready to run further distances.
Remember this is how I determine when to run a horse for certain distances, it may not be correct, but it tends to work most of the time for me
PJR's tactic works also, however I tend to not have the patience to wait that long because I have such a small stable at present. I have only just started playing SO6 after a break from SO5 so if I had a larger stable I would happily wait, as long as the deterioration bar was low.