An EQ, like Wetsounds, is the perfect accessory because it not only gives you the ability to have conveniently located independent zone controls but it allows you to equalize your tower system and in-boat system independently. Plus, you'll like that you can moderate the HLCDs from an equalizer standpoint for near field listening at rest or brighten them for long range wake projection.
Many will use the built-in preamp fader on the source unit if the HU is on the driver's side and if the HU menu allows instant access. Its rarely the case that both work out.
Many of the JL Audio amplifiers have a configurable input section and a port to accept a level control. This way you can select which specific channels the controller operates on multi-channel amplifiers.
A PAC LC-1 RCA line level controller is an option if your source unit is on the driver's side. If not, the Kicker and JL Audio line drivers have remote controllers that are not in the signal path and don't extend the signal path. Eliminates long to and from transverse RCA runs. The line drivers, like the EQ, have the advantage of increasing the line voltage which is often a sound quality bonus.
So you have lots of good options once you have determined your key components and where they will be located.