I number first by the year of the cross, Second number is the number assigned to the cross, and then the letter A, B, C etc. for each in that cross that are kept.
So the seedlings that I just planted are 15 - 1 through 15 - 15 as I have seedligs from 15 crosses. That's the only number they have so far. After they bloom, if I keep let's say 3 seedlings from cross 15 - 2, they would be numbered 15 - 2 - A, 15 - 2 - B, and 15 - 2 - C I keep a master list of each cross number and the parents of them. Of course, if I live another 100 years, I'm going to have come up with a new system!
I think everyone will come up with what works for them.