Setting the gain with a 0 dB tone is the safest way to do it. This way your music can't possibly go any louder. Setting the gain with attenuated test tones (-3 dB, -5 dB, etc.) leaves you with room to turn it up louder for recordings that are quieter overall. If you're running amps that make more RMS power than your speakers are rated to handle you may want to stick to 0 dB test tones.
Always use your ears while setting the gain. Don't just stare at the volt meter until it hits your target voltage.