That depends on your preference and your Route you wanna take 

Sometrains like Eurostar Services from Europe to London or the TGV from Paris to Barcelona or Milan need a prebooking  well in advance. Popular Nighttrains like Brussels/Amsterdam/Paris to Vienna, Budapest - Split, 

Regarding booking in advance or on the Route there are 3 types 

Type A 
Plan everything ahead and book alot in advance (I still recommend to book Hotels with free cancel option) 

Type B 
Plans notheing or just 2-3days in advance :) 

Type C (my prefered ) 
A Mix of Type A & B i have usually every week or every 2nd week a Leisure destination (“Weekend destination”) to relax and have more comfort like Private Room, Washmachines. Between my Weekdestinations i have nothing planned and find my route through several stops. If i notice i wanna stay somewhere longer i cancel my Weekend destination. 

I have usually a Route in my mind but till yet i never did the Route exactly as i had in my mind as i found nice unkown spots, met new  or old friends or got ill on the Tracks :D 

Any websites that are good for cheap hotels or deals ? 

The usual one-best known and best working for West-Eur is booking.com, I prefer it as they do cashbacks and can set to many variables/swipe out or in etc-like also range from cheapest up. Any place with reviews >7,9 (if its not just 1 or 2) tend to be good quality. IF dr. google (which is pretty good for all Qs you tend to have) deliver sites that all only quote US$-skip it, thats not for us. After you have indeed booked via them multiple times (as I have) you get also a kind of status, that will/may give more special discounts or free upgrades etc. Right at this mo I sit in such a place and uses its free wifi.

Young people-the big majority of those anxious/nervous/unsure 1st timers, usually in the past used hoStels=multi-bed rooms, also often good for socialising or even finding travelmates-for a day or longer. hoStelworld (run by that same booking) is good for that, or IF you are YHA and stick to that and its often stiffy similars ´on the continent´: hihostels.com.

In the also not that distant past there were dozens of cheap guidebooks detailing all these points-as about anyone tends to ask exactly all the same again-without apparently even able to think of it all has been asked etc thousands of times before.

booking.com
AirBnb

Hostelworld

Trivago

there are so many :) 

Regarding deals have a look in the Pass Benefits of Eurail as you get some discounts across Europe when traveling with Eurail or Interrail 

I would add Accor hotels to your list - they include Mercure, Adagio aparthotels and the IBIS range, many of which are near stations and often have discount deals - join their loyalty scheme for a few euro discount.

Wow we do not usually get a canvas as blank as yours! How old are you? Are you travelling alone? Are you a £ traveller or a £££££. Are you prepared to stretch your comfort zone and stray into Eastern Europe or do you prefer the safety of the West where you can always find an English speaker?

When I was young I had a  good job so never stayed anywhere other than a good hotel so cannot help you with hostels.  Now I am (a lot) older I have gone off hotels and prefer well equipped apartments and travel with my wife. Apartments mean a stable base for several nights, washing machines so you can travel light and acres of space compared to an hotel. You can choose to self -cater and prepare lunches or go out to restaurants as you wish..

The more information we get the more we can advise.

I usually use booking.com, cheapflights.com, and skyscanner.net.