Hi Vishnu,
Do you have any process called intercompany transfer ??
As far us, i am not sure how you are able to accommodate two different company codes in one order, company codes are two different entities, so system will give an error when you assign the work centre to the operation...
As described in the earlier reply, operation cost are based on the work center cost centre assigned in it, so the labor cost is calculated based on KP26 value... Equipment cost centre will be used for settlement.
Regards
Terence