How do we evaluate the pressure at the bottom? My approach is to add the atmospheric pressure, pressure of the gas and pressure due to the two columns (say of height h1 and h2 respectively h1<h2). This method is giving me wrong answers in questions. Am I supposed to consider only one side of the manometer?
You know the pressure at the bottom of a column of fluid:
$P = P_0 + \rho g h$
In your problem above you have two columns that you could use for the equation, but only one of the columns has a known pressure.
I'm not certain what you mean by "pressure due to the two columns" as you did not include any solution in your question.