Unfortunately it is no longer possible to retrofit the Webasto MultiControl HD to older Webasto Air Top 3500 heater models since Webasto stopped productions on the 'unibox'.
Webasto have replaced this with the UniControl, although your current controller and wiring harness configuration determines which version you require.
Can you please send a picture of the current controller model and the plug that goes into it?
Looking at the Webasto documentation running two heaters from one controller is not supported on older versions like the Air Top 3500. Webasto Air Top EVO 40 and 55 heater models do have this functionality: To correctly run a dual heater installation from one control you would need to create a Master / Slave wiring harness link on the Evo 40 and 55 ECU.