I personally have never bothered to use presets. I just stick to the default 99% of the time. I go into the settings and turn off all the other buttons so if i hit them on mistake i won't get anything.
As for the d-pad, that's personal preference too. Although I have heard if your stick has options to switch between D-pad and stick, and you get used to one of them, changing it will effect your input timings. I don't think i'm good enough to notice the difference, personally, But I always used the stick because I find DP's easier.