The procedure is probably different at every hospital, Bobby, but when I had my treatment at Clatterbridge the procedure was to empty my bladder 20m before my treatment and then drink my three cups of water.
Most men have no real side-effects until quite late in the treatment. I had (I think) 32 sessions, so that took six and a half weeks. I had no real issues for the first four weeks, but after that I had an increasing amount of bladder irritation and a need to pee frequently. The side-effects generally peak around two weeks after treatment ends, and then fade quite quickly. When I was having to pee every 45m all night long towards the end of my treatment I bought a plastic urine bottle (Amazon) so I didn't have to get out of bed, and that was an enormous help.
Very best wishes for your treatment,
Chris