You want to assign an employee to multiple Organizational Units via SAP CRM OnPremise, but do not know how to do so.
You can make use the BAdI method MAP_OUTBOUND of BAdI CRMPCD_EMPLOYEE_OUTBOUND (Enhancement Spot CRMPCD_EMPLOYEE_REPLICATION) on the CRM side to classify the org assignment per employee as primary or secondary.
Also, be aware that one employee can only be assigned to one single org unit as a primary employee (Role Code: 219). However, the same employee can be assigned to multiple org units as secondary employee (Role Code: 222).
If you want to replicate org units with employee assignment, you can assign an employee to multiple org units with the role 222, but assign an employee with the role 219 only to one single org unit in the replication message.
KBA , SRD-CC , Cross Components , How To