A HUGE difference, as to date nobody has made a "Microsoft" Flight Simulator add on that is able to replicate the Airbus systems faithfully.
If you have the FCOMS then that will walk you through the flows on how to set up the MCDU, are you going to be using FMS I or II standard?
The EOSID depends on what your company has paid for in the navigation database, it might be in it... It might not.
Transitions, I would of thought you covered this in your basic flight training... It is not specific to the Airbus... Just think of it as a branch point.. The sid goes to a common point then the various routes from that common point go to a "Transition"
Sec flight plan, depends on the circumstances really, can be used incase you expect a runway change etc etc