Hi Magic Hammer,
If I've correctly understood, previously you had only Windows updates but no updates for Flas or Java. If yes, then:
1. Make sure that you have download PM metadata on "Import Patch data for Windows" page in "MetaData Import Task" place
2. After that you need to choose appropriate Vendor (In your case this will be "Adobe Systems" and check there required products, such as Flash Player) and save changes.
3. Now you can schedule import of chosen vendor updates and get latest updates according to latest available/downloaded PM metadata on your server.
4. When Import task will be completed, open "Bulletins and Updates" report and find there required latest update for further distribution of them.
Thanks,
IP.