I am assuming that this is NEC3 rather than NEC4, as Subcontractor costs are treated differently under NEC4 as an cost component in their own right.
Assuming that this matter is also a CE under the corresponding Subcontract then you would take the Subcontractor's costs and apply them to the components in the SSCC. If the Subcontract was NEC ECS Option A, the Subcontractor should have also included the subsubcontractor costs within their quotation, applied to the components in the SSCC.
You would apply the subcontracted fee percentage to the Defined Cost of subcontracted work (including subsubcontractor's costs) and the direct fee percentage to the Defined Cost of other work.
You don't have fee on fee under NEC3.
I would suggest an instruction to submit a revised quotation, stating the reasons why.