The process of getting a reservation is easy - the biggest problem is trains can be booked solid many weeks before departure. You can obtain a position in the waitlist for cancellations.
I use the following website which is the most consumer friendly and you can use UK credit and debit cards which many sites offering Indian reservations don't accept.
http://www.cleartrip.com/trains
By the way the PNR is the unique reservation code for your seat.
Because many trains cover large distances over many hours or days, seats and sleeping berths are allocated to intermediate stations as well as the stations at the start and end of journey. For instance a train going from Calcutta to Madras may stop at up to 40 stations en-route and each station has an allocation of berths. If you cannot get a seat or berth from Calcutta to Madras then try and break the journey at an intermediate station. You may find you can get two separate reservations on the same train to complete your journey.
Hope the above helps.