It comes down to how confident you are in setting your gains. The higher the number, the safer you are with your equipment. When you tune with a negative db, you run the risk of putting out more power to your speakers or sub than you had actually intended since a lot of music is recorded with a higher db rating. I prefer to stay on the safe side myself.
For example, some rap songs are actually recorded with a + db on the bass rather than a flat to boost the bass in the song. If you tune with a -3 db rating and play that particular song recorded with a +3db in the bass, the amp will be putting out 6db higher to the subs than you had intended.
On the same note, it allows you to boost the bass more with the eq rather than using a bass boost on songs that are lacking in bass as well. Same goes for highs or mids or whichever you are tuning for.
There is no such thing as +3db when referring to a tracks recording, the loudest a CD can go is 0db, that's 0d away from the loudest it can be, hence 0db. If you set gains with a -3 track, the worst clipping you'll get is 3db's of clipping. This means any peak between 0db and -3db on a track will be clipped, between 3db's of clipping for a already 0db spot and at just under clipping, if it was a -3 part of the track.
Most bass heavy music is NOT as a loud as a 0db test tone. Even Jeezy, most Bass Mekanik, etc, etc is around -3 at most of their peaks.. Less bass heavy music, but still fairly bass heavy, most EDM type stuff, skrillex, bassnectar, older and more normal rap, etc, tend to be around -5dbs.
Most music has a crest factor of between 6-15db's, depending on what your listening too. If you like acoustic rock, softer stuff like that, it can go even higher. What crest factor is, is the difference between a source tracks average voltage and it's peak voltage. So if it has 0db tones in it, what is the average level, how much further down is that? That's what crest factor measures.
Knowing this, realize that if you DON'T clip anything ,ever so you use 0db tracks.. On most songs your mids and highs will be 10-15db's down from their "RMS" number on the box. (the peak voltage you set your gains with the DMM with).. So, let's say 12db to pick a number in the middle of that range. That corresponds to 1/16th the power.. So if you have a nice 250 watt amp on your mids, the mids will on average, being seeing 16 watts. They might see the 250 the speaker is rated for for only a very brief spurt of time (like less than a second, think a hard drum hit or loud vocal passage).. Clearly that's not how they rate speakers when they are using "RMS". Now if turn the gain up a bit, another 6db's worth, we now have a bit of clipping. We've also allowed our speakers to see 62 watts on average, and much closer to maximum power a majority of the time..
Subs work the same way. Yes, sub content tends to be less dynamic... However, subs are also much less sensative to clipping. Mostly because they have larger coils that handle more power easier. The extra power that occurs during clipping, some of it is higher order harmonics of the original signal, distortions. Most subs however have high enough inductance most of this "extra" never makes it out of the speaker, the coil inherently filters it out so you don't hear it. Also, since these harmonics are still relatively low in frequency, your ears don't notice them much anyways.. Lastly, even order distortion is the least offense to the ear and often just sounds warm.. Think about how electrical guitars sound, that is warm even order distortion from an amp. Long story short here, if you set gains with 0db tones, you either are
A. A serious competitor who is using 0db burping tones to see a number on a meter
B. An idiot who likes wasting the power he paid for
C. Someone who really never listens to music at any appreciable volume level..
D. Have amps rated at at least 2x the power rating of the speaker, really to not fall into category B, you'd want to have 4-6x rated power.. So yeah, if your running a 500 watt amp to your 125 watt rated midbasses, don't bother clipping.. Set gains with 0db tones and 500 watts worth of voltage and you should be good to go.
A little clipping isn't that dangerous.. I could write another post this size about why setting gains with a DMM is a silly *** idea, but I'm not going to bother right now. If you insist on setting gains that way, instead of using your ears and common sense to maximize equipment from song to song... Then at least use a -6db tone. -3 if you REALLY worried your going to break something and listen to nothing but hardcore bass heavy rap all day.