Analyzing different lines of your game

I am wondering how I should be analysing different lines of my game. 

Often I try to find out how to game should have gone when I played a different move at a certain position. I always struggle in finding an effective way of doing this. 

I can of course use an engine and it will propose the "perfect" line however should I do this? Or is it better that I come up with alternative line and use the engine to compare which one is better or worse. This way I can actually learn something as I come up with the line and not the engine. Eventually I can compare it with the line proposed by the engine to see what the thought process is (if I can follow it). 

Basically, I am looking for some tips on how to analyse your own game and not just find mistakes but find better lines.