Like Mike said, the tower zone gains will be set independent of the in-boat zone. Why? Because you want the tower to hit the sweet spot between low noise and high dynamic range instead of being governed by an alternate zone. You are not trying to balance it at straight up on the fader with another zone.
There are three basic tuning methods.
1) A CD or downloaded sine wave at the correct and different frequencies for fullrange speakers and subs. You would use a voltmeter to set the voltage limit of the amplifier with no speakers attached according to a formula and according to a known amplifier power at a particular impedance and at a particualr supply voltage. You want to avoid this method unless you have those accurate numbers. This works with JL Audio amplifiers because they will meet their 14.4 V spec even at 12.6 Volts. Because the JL Audio amplifiers are so conservatively rated we usually tweak this by ear afterwards. I would avoid this method unless you are given realistic, hard numbers. Otherwise you could do damage to your speakers.
2) The same CD or download with a handheld O-scope or distortion analyzer where you measure the amplifier output to the maximum pre-clipped level. Either measuring device will detect the first signs of a sinewave as it begins to square off (clipping).
3) Tuning by ear where you are the instrument that detects initial clipping/compression. In this case you are using dense and dynamic music.