Temperature is the measure of the flow of energy, particularly of heat. When you put two things of different temperature in contact with each other, they will eventually have the same temperature (thermal equilibrium). What happens is that heat flows from the hotter object to the coller object.
For example, in your first beaker containing hot water, it will eventually cool to room temperature as heat flows from the hot water and beaker to the surroundings. At this point, you may notice that the beaker is also hot (it is probably in thermal equilibrium with the hot water).
The cooling rate depends on the heat capacity of the substances. The lower the heat capacity, the quicker heat is gained or lost (depending on the situation). Now, if we want to know the difference in rate of cooling of a single beaker and a lot of beaker packed closely together, we simply have to note their heat capacity. Note that heat capacity depends on the mass of the substance. Assuming that the entire system (beaker + water) is a single entity of a certain heat capacity, the single beaker will cool faster than the group of beakers. [Of course this will change and will be different if the beakers are far apart from each other].