1. I studied in textbooks that the boiling point of water is the temperature at which the vapor pressure is equal to the atmospheric presssure. My doubt is since the vapor mixes with atmosphere, how can we say vapor pressure is equal to the atmospheric pressure. Please explain this concept.
The vapor pressure of water follows the Antoine equation, which is given by:
$ln(vp) = A - B/(T+C)$, where the constants A, B, and C, are different for each pure chemical species, and T is the temperature of the liquid in question. The vapor pressure of water is dependent only on temperature, and is independent of the atmospheric pressure. As the temperature of the water rises, the vapor pressure of the water rises. When the vapor pressure of water is equal to the ambient pressure of the atmosphere above the water (also, please see qualifiers in answer 3 below), steam bubbles that are formed within the water have enough pressure to avoid being collapsed by the pressure exerted on them by atmospheric pressure, so they rise through the water column that contains them, and exit the water as steam.
2. What are the causes and conditions for the formation of bubbles while water boils?
The cause of boiling is heat input to water that is at its boiling point. This requires a nucleation site, which is a very small "void" (i.e., microscopic in size) on the surface of a metal pot, or some other small imperfection in the surface that the water rests upon. This is the exact reason that you should never heat water in a microwave oven, in a very smooth container. The lack of nucleation sites in the very smooth container ensures that the water becomes superheated (hotter than the normal boiling point), and any small disturbance to the water (i.e., jiggling it as it's removed from the microwave oven) causes it to "flash" into a mixture of water and steam, probably scalding the person who removed the water from the microwave oven.
3. In many textbooks atmospheric pressure and vapor pressure are related to boiling. Why does the pressure of the liquid not affect the bubble formation?
For a "deep" container, the water column adds additional pressure to the water that is at the bottom of the container. Due to this pressure, the water at the bottom of that water column must be heated to the point that its vapor pressure overcomes the pressure at its location, meaning that a sea level container with several inches of water in it must be heated a few degrees above 100 C to get the water at the bottom of the container to boil. This means that the liquid that is above the steam bubbles that are forming, does indeed affect bubble formation.