Hi,
As per my understanding, while creating intercompany billling you want to add some mark up value for the hours booked. If my understnading is right,
1) You can add conditiopn type for mark up & the values for mark up condition type is posted on the same wbs element on which you are booking the cost.
or
2) you can maintain the condition record for price in addition with the mark up value for the specific criteria.
Kindly check & revert,
Thanks,
Pankaj