The above advice is certainly sound and cube hopping is a great way to end up with different beers from the same wort or to try different hops to see what they bring from the same base but I'm not a massive fan of what they leave behind in the cube.
For hoppy beers I generally use a very small bittering addition, around 0.5g/L and then a large addition into the whirlpool where after flame out I have let the kettle temperature drop to around 85C but definitely under 90 and then whirlpool and stand for about 30 minutes, then dry hop for aroma. I find that this gives me the best results in terms of flavour and bitterness.
For other beers that don't have massive late additions like a pilsner or lager I normally just go with a bittering addition and a 15 minute addition with a ratio of 1:2 and quantity depending on aa%. Often for these beers you are working with low aa% hops and lower IBUs which, in my experience, are much more forgiving!
In my experience there isn't any brewing software that adequately deals with the complexity of hop additions from flame out onwards and so you really need to have a play with it and come up with something that produces the results that you like and is repeatable.