Component designators on multi-pcb projects
I had worked on similar kind of project before having 3 boards that are interconnected. 

Even though 3 boards... as far as schematic conserned we usually make a common schematic file.. with sections 

So going with continuous designation is good.

I feel this way comfortable.


  The boards are going to be panelized and sent off to a pick and place in china, so how would it work if you had two boards with designators that start again?


It is also not a problem with pick and place machine what ever your approach.

But going with continuous designation approach is better for BOM management(inventory), Diagnosis etc. Since in every case you need to consider any component with the whole schematic. it leads to less confusion.