I'm not sure in regards to the bulk import as I'm not sure if you were referring to a manual export/import, connector rule setup, or replication. Regardless, if they have the same serial number, system number, or barcode information in each record and the system does not auto merge the records, you could run the built-in Duplicate Computer Merge task to merge the resources based on whatever merge key you specify.
Regarding the organization issue, I prefer to manage systems based on a custom organizational view and sub organizational groups. I've created some automation policies that dump the computers into the correct grouping based on OS, domain, or AD OU. The organizational structure I'm using is:
Company Name
Clients
Servers
System Objects
I like using the org views/groups method as it allows segregation of duties based on a security role.