Amtrak terms and conditions state that if you fail to board your train as booked your entire reservation is subject to cancellation
It's one of the first things detailed on the conditions of carriage page here.
http://www.amtrak.com/servlet/ContentServer?c=Page&pagename=am%2FLayout&cid=1241337896121
If discovered that you boarded at the wrong station the conductor at the very least might ask you to pay the difference in fare, and possibly be forced purchase a whole new ticket.
You ask about changing your ticket.
All saver fares are non refundable, so you can't change the booking, however if cancelled in advance they will issue you an e voucher for the value of the fare. Value fares also have conditions about cancellation and refunds
You would then need to purchace a whole new ticket, and if the saver or value fares have already sold out then you will be forced to buy a full fare ticket