Hi Tsvetelina,
if you want to upload master data you need to define the communication systems. So please create one with flag SAP Business Suite system set for the ERP system and one without that flag for the non-SAP system. The best choice for the ERP system is to use the logical system ID of the ERP system in both fields IDOC logical System and also in the System Instance ID. Communication arrangements are not needed for file upload.
If you upload employees with template Employees for Travel you can modify the source system in the properties after you uploaded it to Cloud for Travel and Expense. There you also can use non-SAP systems. Please maintain the deviating source system for the cost centers in the details of the template. As far as I remember for cost centers it is not necessary to specify the deviating source system of the manager.
Best regards, Reinhard