Regardless of amp and speaker brand and speaker type, the gains need to be set using one of the 2-3 common methods.

Tower amp, in-boat amp and sub amp: All amp gains need to be set independent of each other. Doesnt matter to the in-boat amp that the tower speakers were not installed yet. If your dealer had trouble setting the gains on the in-boat amp because the tower speakers where not installed.....I would find a new dealer to do the install.

What is it about the setup that you are not happy with? Gains are typically a set it and forget it. Cross-over filter for in-boats and towers should be "HI-PASS" and "LOW-PASS" for the sub. The cross-over frequency will have a ball-park range, but now exact setting. For the in-boats, I would probably end up somewhere between 80-100 Hz. For the towers, about the same, 80-100hz. For the sub, you should set it close to where the in-boats end up. This creates a smooth transition.

Also, keep in mind that the ZLD is a line-driver, so your gains should end up lower then those with the same amps, head-unit and speakers, but no line-driver. head-unit and EQ settings need to be flat or zero.