The only way from Katapola (Amorgos) to Alexandria is by flight. You should expect to be able to find tickets starting around $280, if you search flights from JTR to HBE. The best time to book shorter flights is 2-3 weeks before your trip.
On your trip from Katapola (Amorgos) to Alexandria, it is best to book as soon as possible. It won't necessarily help reduce your price by a large amount, but will ensure that you have a spot on the bus or train.