wow, you're swimming way under water
it's all driven by database settings and designed for stability (hence the re-syncing of state on each reboot, to avoid issues with transient errors). this is after a lot of experience to make things more stable.
honestly, though, i am not sure if amahi is for you at this stage, i'm sorry to say
this is not to discourage you at all. but the amahi system is designed for a simpler, less complex network structure than what you seem to have. and it's meant to be managed via the web interface.
now - let met get to the point.
the settings are in the mysql database and they are propagated through the system any time settings are changed.
(i should say that that propagation is sub-optimal at this stage, as it's a bit too broad and it could be improved in a number of dimensions.)
anyway, hdactl writes the settings on demand by the system.
the "right" solution would be to know what you want to achieve and figure how we can support it through the web interface. in the setup area, under networking, there are ways to assign static IPs, to add aliases, etc., etc.
maybe it is not too hard to support!?!?
alternatively, we were talking on IRC and perhaps we could have a solution (courtesy of relrobber) to have a setting to "freeze" the dhcp (and perhaps other) settings. that may work (at least for you anyway

)
this is a sensitive area, as it can impact reliability/stability (a big deal on a server that it's working 24x7 or nearly), so we want to tread carefully!