Mayuresh,
You should understand that distillation and fractionation is affected by the L/V ratio (or V/L ratio) in each section of the column. However measuring the V and L at any point inside the column is not possible. The reflux flowrate however is easy to measure, and therefor the equations in hand methods like McCabe-Thiele are written in terms of reflux ratio R. It is then asumed that V and L are constant in each section of the column: equimolar overflow, so L/V ratios can be written in terms of R.
The boil-up ratio is also important, but as it cannot easily be measured hardly anybody talks about it. You probably never heard of it.
But reflux ratio and boil-up ratio are related in McCabe-Thiel: if you know one, you can easily calculate the other. In fact: one could rewrite all equations in terms of boilup ratio instead of reflux ratio. But because boil-up ratio can in practice not be determined, nobody does.
In reality however there is no equimolar overflow, so simulators don't work with equations based on R but rigorously calculate V and L at each theoretical stage (usually from the stage heat balance) and use those, together with the K-values of all components, to calculate the separation in the column.