It kind of depends where you plan on playing but if you can have everything as wav (or flac) that would be best. A lot is made of the difference between mp3 and and lossless but tbh if the mp3 is 320kbps most people can't tell the difference and I found that it's only in a club with a big soundsystem that you can can hear the difference and even then its most noticeable when you mix from a wav to an mp3.
With naming conventions I always did artist first then track name as I never remember track names but always remembered songs by the producer, I don't think there's a right or wrong but I put an underscore instead of the spaces in the name (artist_track_name) as this usually makes it easier for different systems to read files without adding weird symbols (it's not likely but I remember copying files from mac to PC and things got scrambled)
How you organise things is the most important, do you group by BPM/Key etc that's just going to be a bit of trial and error to see what works for you, what I would advise is that if you play out you take a record bags worth of tracks (no more that 50) on a USB stick to make it easier to play a set, if you've got thousands of tracks sometimes you can get paralysed buy too much choice or just lose flow in a mix by being too all over the place.
Anyway I haven't DJ'ed in years so feel free to ignore everything I say :)