I use wind up because that's the way I learned to do it. I find it totally intuitive and easy.
Makes no difference IMHO which way you use it, just use the way you're happiest with.
That said I now tend to use Navbox Pro 'cos it does everything else for me as well, including looking up and printing the frequency list. Also does w&b and fuel burn and is less prone to artithmetical errors.
However before you start doing that make sure you are totally at home doing it the mandraulic way, then you won't get caught out if plans change.