Hello cyoung123. A very warm welcome to the Coffee Shop forum.
If you plan to buy Advance Purchase (AP) tickets then these will automatically come with a seat reservation. AP tickets go on sale
up to 12 weeks ahead of the date of travel. Generally, the earlier you book the cheaper the fare. As of today First Great Western's Advance Purchase tickets are on sale up to 12th August 2012, 9 weeks hence. You are unlikely to find very cheap AP tickets if your journey involves travel in the peaks, particularly the morning one.
Travelling 3 days a week using AP tickets bought as far in advance as possible may still be more expensive than a weekly or longer Season Ticket - it all depends on the times of day you will be travelling. Season tickets will give you ultimate flexibility on when you travel and they have the added bonus of being valid to any station on the line of route between origin and destination, so may be useful for leisure trips - even to off route destinations by just paying the fare from where you diverge off your season ticket.
Do note that AP tickets are non-refundable and should you not travel on a particular day for your own reasons then any AP ticket purchased for that day becomes worthless.
There is also the slower and generally cheaper route via Salisbury to consider if the times of trains are conducive. Remembering that it is easier and quicker to get from Waterloo to The City than it is from Paddington.
More details on the times you will be travelling, as well as your ultimate destination in the City of London could be useful in finding you the best and cheapest options.