Sachin,
It seems you are dealing with plants abroad situation.
Based on the above description I see you are using ECC to trigger the declaration not the TM.
you need to do an enhancement to determine the right FTO.
If France Entity owning the plant in Italy with FR VAT No?
you can define some dummy company code - like FRIT - and map your FTO as FTO_FR10IT - Plants abroad for France Entity - IT in the FTO represents which country this plants abroad belongs to.
Now - you need to put the customs code in a BADI to determine the transaction flow and change company code to FRIT when the document flows into GTS.
you might also need to change couple other fields on the declaration - you can use header data proposal BADI to do this.
If you are using TM - you have to deal with with Responsible Org and Processing Org Business Partners.
Responsible Org - is nothing but your selling entity
Processing Org - is nothing but the Plant business Partner
Once you get this info into GTS - you can determine the company code based on the transaction flow and reflect the company code you want to see.
My number - +16146204465. Thanks.
Regards
Rajesh