Are you on a non-flexible ticket - Europa-Spezial Niederlande, or whatever they call it on the NS site? If so then the fare will be the same regardless of what station in the Netherlands you specify as your starting point. I would specify Eindhoven as the starting point, because....:
- you say you're more likely to start your journey there
- the fare from Amsterdam to Utrecht is less than the fare from Eindhoven to Utrecht
-.the ICE train starts in Amsterdam. If you have a ticket from Amsterdam then your reservation (if you get one) will start from Amsterdam. If you have a ticket from Eindhoven your reservation will start from Utrecht because that's where you're getting on the ICE
BTW, although saver tickets are tied to a specific train you do NOT need a reservation. It's recommended, especially in second class, but it's not compulsory.