If I've already bought a eurail pass, can I only make reservations on the rail europe website to get the passholder discount or can I use other websites as well?
If the train starts and/or ends in Germany, you can get passholder "reservations" on the German Rail website. Of course, for most German Trains reservations are only seat reservation, not supplements, are not required, and you can get them for the same price at the counter, €5,50 per seat in 1st class. It's an entirely different story for night trains. They are very popular and passholder accommodations often sell out a month or more in advance. Again, you can get reservations online from the German Rail Website. Reservations for trains in other countries might not be so easy to get. If you have enough reservations, you can always get them through Euraide. They charge $50 for handling but you pay the European counter price, which is often a lot less than Raileurope's price.
You can use other websites if you wish. If you are traveling during the day you can make them at a ticket office in Europe. If in France you can go to SNCF Boutiques which are in many towns throughout France. They are on the high street, not in the station. You can also use travel agencies in many European cities.
When we arrived at our destination, we asked questions and made needed reservations for the next leg before we left the terminal. Some of the more used routes and times sell out quickly. Except for one information desk, we got good information and helpful information from the terminal workers.