One Data Pool with data from SAP ECC and S4H

Dear All,
Could you help me with the following issue?
We extracted P2P data from SAP ECC and S4H using ABAP scripts. So I have two sets of exactly same tables related to P2P process.
The reason for doing this was, we have different company codes processed in ECC and S4H.
Now we we want to upload them using SAP ABAP Output Uploader into one data pool, and finally combine into one data model.
Seems like it does not work, because the S4H overwite the previously uploaded ECC data due to the same table name uploaded.
thank you in advance