You seem new to this, and apparently you're referring to the individual speaker levels (channel settings) when you mentioned decibel settings, and master volume as volume settings. My suggestion is just run the calibration and let it do its work, you paid for it to do so, and more likely you'll get THE correct relative channel levels. Then set the volume setting to a comfortable level or just loud enough without obvious distortion.
Tweaking is optional, but it would be wise to write down or memorize the settings beforehand.
As for the dB volume settings in an amplifier, the calibration starts down from -XX dB up to 0 db, with 0 dB representing the nominal Maximum rated Power of the Amplifier. So a -3 dB setting on the amplifier volume is 1/2 of the Maximum rated amplifier power (log(0.5) * 10 = -3), a -6 dB setting on the amplifier volume is 1/4 of the Maximum rated amplifier power (log(0.25) * 10 = -6)
Not all amps/receivers use 0dB volume setting as reference level. Different manufacturers use their own scaling, some start with zero and max at 80, some range from - something to zero or + something, etc. Even some manufacturers implement different volume scales among their receiver models. Without the proper tools or documentation, we will not know exactly what volume setting is the reference level.
Also, a source material that is recorded hot (more than 0dB reference, think loudness wars) may max out your amp even below reference volume setting.