You can control the order that they enter by switching them around on the pre-battle screen.

When I'm defending I usually let my archers empty their quiver then withdraw them for some cavalry units for flankage. Also I withdraw a unit if it's very tired, get a fresh sword unit in there to take its place.

If you're in a battle with multiple stacks on both sides that's going to have more than a few fights within the battle you may consider withdrawing most of your army for fresh reserves. Just make sure you got it set up so you can get the correct types you need i.e. don't withdraw your very tired Katanks for some fresh woodsman