You should prune fruit trees at planting time (i.e. when you plant them in the ground). However, if they are getting tall and you plan to keep them in pots, then you can prune them in the pots. For new fruit trees, if training to an open center, you should top them at planting at about 30 inches high to help balance the top of the tree with the root system and to stimulate branching. Typically pruning is done in the winter months when the trees are dormant, but you can prune during summer. Winter pruning tends to stimulate new growth, whereas summer pruning can slow growth. My recommendation would be to plant them in the fall or late winter, and then prune them before bud break next spring. For more information on pruning, you can refer to this OSU Extension publication: https://extension.oregonstate.edu/catalog/pub/pnw400. For more on growing tree fruits in home gardens, refer to: https://extension.oregonstate.edu/catalog/pub/ec-819-growing-tree-fruits-nuts-home-orchard.
One other note to keep in mind, apples do not grow true to seed. Meaning, that the fruit from the new apple tree will not match the fruit from the parent tree from which it came. You could get lucky and have a new tasty variety that develops from it, but most likely it will develop fruit that is of poor quality. The peach should be similar to the tree from which it came.