Hey,
I start with a few chords or melody which I like, record them into Cubase, then start adding/removing stuff along the way. Eventually I try to remove the sounds of the initial chords and replace them with more exciting sounds, or try to not make the chords sound so 'obvious'.
As for the percussion, I usually just sequence something dumb at the beginning to have something to work with, eventually I replace that with a better programmed beat or a sample(s).
Basslines? Usually I do that in tandem with the melody.
The big thing to remember is that there isn't a right or wrong way to do this, the difficult thing is finding a method which works with your style.
Take care,
Nick