Hello Dharmesh,
A BSG can consists of more than one source systems as per design. But if you look at /SAPAPO?MATMAP table the key fields are Client/Product/Product type/BSG and this is linked to the Logical System in the same table. Now if you have one BSG and same material is there in both the R/3 systems then there will be a conflict. Same with the //LOCMAP table.
So my thinking is you can have multiple ECC with one BSG if products AND locations are mutually exclusive in both the systems.
If you have same products in both system then use different BSG same for locations...
Regards,
Abhishek