The puja room is the most important place in the house. It is the place where the Gods are worshipped and has that significant vibration due to this and hence it calls for a separate space within the house.
The whole of the universe is made of energy. What we see and worship as God is infact the superior form of positive energy that vibrates within the universe. We all yearn to obtain the maximum of this positive energy or blessings of the higher souls. Hence the puja room should be that kind of a place where is not disturbed by other activities which can dampen the power of the positive vibrations generated in the puja room.
When we worship the Gods in the puja room, our actions generate positive vibrations through the chanting of the mantra and other rituals performed during the puja. This would have a calming effect on the minds of the inhabitants and provide them the right direction in life. Hence this room should be kept far away from the bedroom and bathroom which can create negative vibrations due to the acts of tamasic nature performed within those rooms
The puja room when kept clean and maintained as per rituals, generate huge positive vibrations and fill the house with sattvic energy. This energy remains always present in the room and can be harnessed whenever we feel the need for it. This is the reason that when ever we spend some time in a puja room we feel more calm than before. This can provide the same effect as that of visiting a temple and performing the puja.