You will need to clone the stored procedure, clone the report, point the report to the cloned stored procedure, and then modify the stored procedure to meet your requirements. You can pass parameters to the stored procedure just as you can pass parameters to a SQL query.
You can find the membership filters by searching in the top, right-hand corner of the SMC. Then view all filters and right-click and open the filter in a new window. For example, here's the SQL for some random Java update:
SELECT _ResourceGuid FROM Inv_Applicable_Windows_Software_Update WHERE SoftwareUpdateGuid='9a056f38-7a44-411b-ba44-9b2c95e8c786' and _ResourceGuid not in
(select _ResourceGuid from Inv_Installed_Windows_Software_Update where SoftwareUpdateGuid='9a056f38-7a44-411b-ba44-9b2c95e8c786')
(This was performed in Patch Management 7.1 SP1.)
Does this information answer the questions you had?