No,When Subject based registration is active then  the corresponding subject amount is calculated only.We don’t have provisions to set handling charges.
But you can always do that by adding that amount in the subjects itself.


For Example

Case 1

Cost for                      Estimated cost of registration

Subject 1                        $200

Subject 2                        $200

Handling                          $50


Case  2


Subjects Opted for       Estimated cost of registration

Subject 1                           $225

Subject 2                           $225


The requirement of case 1 can be met by revising the subject amount  as case 2.
Note:-In such a case one can also use the instant fee collection in the fees section.