A Partner Billing Rule "charge" can be applied to the customers' bill in one of two ways:
1) As a flat fee
2) As a % of spend
If the charge is being applied as a flat fee, you will see a line item present within reports for this billing rule.
If the charge is being applied as a % of spend, you will see that this charge is built into every line item for the customer. To verify this, you should compare the subscription costs at the Partner and Customer levels.