Magento Integration -Will your link work with a muti store magento 2 setup?
Depends how you have that configured. If it's 2 stores in the same Magento instance - only store Ids / website Ids change - then that can be configured in one DSYNC account.
If you have two different websites, it is also possible but we usually configure in two separate DSYNC account.
Also, depends what you would like to synchronize and what Magento version it is. Multi store inventory for example - as you know, M1 has global inventory levels and yes there are plugins which allow you to have multi site inventory levels however our connector works with vanilla Magento installation and would not 100% support this. With M2 (2.2 EE) we do have a solution available for multi catalog.
To answer your query better we'd have to know what exactly you want to sync (with which system), and version of each system + any custom extension which may impact integration.