Question

how we will know that in a right angle triangle which is the perpendicular and base

Answer 1

Both perpendicular & base are same. You can take any of them because both form 90 degrees. Or you can take the longer side in them as perpendicular or height 

In the case of trigonometry, dont use them as perpendicular and base. Use them as opp., and adj.  For example, Sin p = perpendicular/base = opp./adj. That means if they gave sin p, take the opposite side and adjacent sides of that angle