All travel agents are selling from the same shelf, if I can put it that way. They don't have their own allocation of holidays from any particular operator. Operators' packages are available to all approved agents, and once they are sold, they are sold. Thomas Cook do have their own specialist operation, being both an agent and a tour operator, but you could book a Thomas Cook operator holiday at a Lunn Poly shop. The foregoing applies to brochure packages, and the best to go for would be the one offering the best discount/free insurance/whatever.
When it comes to flights and hotels booked separately, it may well be that a particular agent has negotiated a deal with an airline or hotel chain that means they do have a better discount. You need to decide what you want to do, get both agents to price it for you and take whichever is best. Both are competent agents.