Let them make their own charge (don't over use the double-clicking). Fatigue level is increadibly important in RTW so conserve energy. I personally don't like having my cavalry go to waste by going through an enemy unit, but against light infantry (such as akontistai) in open formation, it has its uses.
As for letting them stay in melee, that depends on the situation. If you think the pressure of having that cavalry unit there in the melee will make the enemy rout, stay there for a bit. If you see that that isn't gonna happen, withdraw, reform, charge and then the classic "rinse and repeat" for as many times as necessary.
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