It varies depending on what kind of song you’re doing. As for those specific questions, I always make MIDIs of the songs I’m covering in advance in FL Studio, though in some cases I use pre-made base ust/vsq files made by somebody else, so I don’t have to fiddle with those things in the program. Really, you could make your base files in the Vocaloid editor, it’s particularly easier in V3 where you can import .wav files, but rather than being harder it’d just be slower than using other programs.

But, I can’t really make a fair judgement on the difficulty of using the program, I’ve been using Vocaloid for 1½ years now, and at this point I’ve learned a lot from my experiences and tuning is almost automatic for me now. Of course, everything doesn’t always go smoothly, but I believe I’ve learned all tricks necessary for my particular tuning style.

If you imagine it as sort of a graph, as tuning skill goes up, your tolerance for untuned vocals goes down, and you keep pushing yourself to work more on the vocals.