Hello Krzysztof,
I am sure how each person uses lilypond is a very personal thing, since it is so flexible. I engrave quite deeply complex New Complexity School keyboard music in the main, as a serious professional undertaking. I simply use multiple voices for treble and bass staves, sometimes up to six or seven per staff, and also sometimes breaking out into three or four staves per system for clarity. Using Frescobaldi makes all this terribly easy and I have therefore never stopped to think about it. For my work, I colourise each voice with a different colour so my brain can untangle the complex braids of the music. I just turn this off when ready to publish. I find that helps greatly.
Andrew