Rick Steve’s “Europe through the Back Door” is the classic “how-to” on traveling in Europe, and any backpacker-oriented guidebook is going to have ample practical information on how to get from place to place, etc. Grab a Lonely Planet and read all the stuff that is around the reviews and city guides, and that will give you pretty much all the information you need.
It’s been a while since I’ve travelled in Europe, but my travel style is pretty loosely planned. I like to be able to stay in a place as long as I like, and move on when I get bored. This doesn’t work if you have an extremely tight timeline. But if you have enough time to wander a bit, it’s a great way to travel.
So I typically book the first and last night of a trip (you want to know where you are sleeping before you fly out!), and play it by ear from there, using hostels.com or hostelworld to book a day or two out. I’ll usually only book a night at a time, so that I can move to a different hostel if I don’t like the one in in. Most hostels will let you tell them in the morning if you plan to stay another night.
I pretty much do the same with transportation, buying tickets as I go along. The nice thing about Eurail passes is you don’t have to book (unless things have changed). You just hop on. I do a lot of night trains because it saves on accommodations and gives you more time, but that works because I sleep well on trains.
My biggest suggestion is to keep your ambitions modest in terms of the number of places you go. Have a deep experience in a smaller number of cities rather than a superficial one in many. Train stations, checking in and out of hotels, packing and unpacking, etc. are all stressful and not fun. Do less of that, and you have more time to do what you actually came to do.