Yes, you will keep your current players. It will only replace existing players if you lower the amount of players from a certain age group. If you don't, no problem at all.
Let's say you have 5 and your new amount, according to the custom youth setup, is 3. 2 of the existing players will get replaced at random then.
But if you just increase the amount, the existing players will be kept and new ones will be added.