New Post: Using Catalogs

Everything imported fine but it created a new Adobe Systems update section ...

This is because packages in Adobe's catalog are published Under "Adobe system, inc.". And you have probably published your own update Under "Adobe" or "Adobe system Incorporated". If you have published from a MSI or MSP file, then the company name used is "Adobe system Incorporated".

...and didn't supersede the old one.

This is by design. Updates in catalogs are not marked as superseding.

My first question is what would best practice be here? Decline the old updates and approve the new ones?

You should apply the same Policy than you apply for Microsoft updates.

My second question is if I import from catalog again, would it supersede the updates that were imported from the catalog the first time

No, you have to manage that by your own.

How do I find the catalogs to subscribe to? I would love to have them for Flash, Reader, and Java.

Open WPP, go to "Manage Catalog subscriptions..." - > click on "Load a shared catalog.." -> choose your catalog.

As far as I know, there is no catalog for Java.