-yes I have adjusted the tone.
What tone did you adjust?

Just note, the "base" in the base, mid and treble menu, has little impact on the woofer and mostly impacts the full range. SO dont jack the "base" trying to improve the woofer.

The Sub level control in the head, is linked to zone 1. Its a sub menu, pardon the pun. So if you turn down zone one, it reduces the subwoofer level also. This can be a downside for some systems.

I would not worry about left to right balance. It needs to be centered. if one adjusts balance left and right and hears the volume change between tower and in-boats, something is WAY off on the signal configuration.

With 4 chnl and 2 zone output, FADE is now called 2-zone control. No need, or place for, fade any more.

For the 2 zone control to effectively work on an in-boat/tower setup, ALL speakers need to be powered by external amps. I am not overly familiar with the Moomba audio options. However, are their one or two grayish amps mounted and wired on the amp wall in the port locker?

Phones connected in what way? BT, USB or old school AUX cable?

Odds are, the entire system is setup less then ideal and poorly tuned, which includes a woofer setting within the head, that not may know about, or how to setup.