You are not able to find option to add Material Valuation for existing Materials using Migration tool for Materials.
This is expected system behavior. Migration tool for Material Valuation and Mass data Maintenance for Material do not provide option to enhance the data.
The data could be uploaded only as a one time activity. The same can't be enhanced later with Migration tool.
You can use below options to enhance the material valuation data:
1: Go to Inventory Evaluation workcenter
2: Select the button Import cost unit
3: Now select the option From Microsoft Excel and import
Option B) You can also use Web service ManageMaterialValuationDataIn to enhance this
KBA , AP-SVO , Service Order Processing , How To