Here are the basics of researching rail travel and prices in Europe. Before you consider renting a car for a trip, always follow these steps.
1) Forget you ever heard the words "Rail Europe." They are a reseller, they do not list all tickets, and they usually mark up the tickets they sell, sometimes substantially. Unless you have a VERY specific reason to use them, don't.
2) To find train routes schedules for almost all of Europe, use the Bahn (German Rail) website http://reiseauskunft.bahn.de/bin/query.exe/en, following Rick's tutorial: http://www.ricksteves.com/travel-tips/transportation/trains/online-schedules
3) That site will only have prices for trains that start or end in Germany (such as yours). To get the best possible prices for other trains, you almost always want to buy from the website of the country where the train originates, although there are exceptions. Here's a great list, from the rail guru The Man In Seat 61: http://tinyurl.com/bo8x6o6
4) Most international trains, and faster domestic trains in France, Germany, Spain, Italy and England (among others) have discounts (often massive) for advance purchase, if you can work with non-refundable and non-exchangeable tickets (or with significant restrictiond on those actions). Domestic tickets in the Netherlands, Switzerland, and Belgium (with a few exceptions) do not have discounts for advance purchase.
5) For some places like France and Spain, it can be a bit complicated to book train tickets online (if you need these post your route here, and we'll help with the tricks). But the Bahn website is easy to navigate. You book the ticket with a credit card, get it in your e-mail as a PDF, and print it at home (it says you need A4 paper, but 8.5 x 11 works fine). On the train, you show the printout along with the credit card you used to book the ticket. The conductor scans your ticket, swipes your credit card, and you're set. For two or more traveling together on advance discount tickets in Germany, the discounts are even greater than for solo travelers. When my mother and I went from Berlin to Dresden in 2012, the one way full fare was €38 per person, but the one way advance purchase was €19 for one person and €29 for two. So, with advance tickets we saved €94 on that one round-trip alone!
6) A quick trick to find out whether or not a particular train has a big price difference for advance purchase: look at prices for your dates, then for later today or tomorrow. If you can live with the last minute prices, no need to pre-book. If you want the discounts and can live with the restrictions, book ASAP (once the cheap tickets are gone for a particular route, they're gone).