Hi Mathew,
I would recommend you to create the Sales Order via custom program that runs periodically (for automation) at regular time intervals and checks what sales orders have come up from other system and the code for the split should be written in the Custom Program processing the sales order/ , and then after use BAPI_SALESDOCU_CREATEFROMDATA1, based on the required data coming from the other system// in the interface that runs on R3 we can do that i.e. the code that would be written in custom program can be used in the new interface running on R3 side.
This will solve your purpose, please validate the same at your end as well, let me know in case any further inputs are required from my end.
BR/Thanks
Pranav Agrawal