From your description, the smart relay sounds perfectly suitable for a dual battery setup.
If that's not a typo, 12.4 at the coil when you've got 13.5 at the battery is too low (13.5v is also low at the battery when idling). Is this a kombi? If so, the problem is that the voltage for the coil comes from the battery the long way - via the ignition switch! The low voltage is probably b/c of corrosion on the terminals. Clean the fuses, where the battery earth strap joins to the body and the terminal on the solenoid where the battery positive connects. See if that helps.