Dear Guna,
Please clarify whether the source system going to be your BW system or R/3 system ( Your subject line is contradicting with your detailed message).
If there are multiple BW system getting hooked up to your source system, then your datasource wont have any issues in providing the data to both the system. You can see that tables likes ROOSPRMSC, ROOSPRMSF stores both the source system as well as the DWH System details which is nothing but your BW system.
Regards
Gajesh