You can update Flash Player and Adobe Reader via Windows Updates using SCUP through WSUS/SCCM.
Then once installed and configured on your server, you can connect to the Adobe catalogs for Reader and Flash Player and publish them to WSUS/SCCM to be pushed out via windows updates.
You will need to add a local or group policy though to enable signed intranet updates to apply to your users machines. I’d recommend group policy as this will then go out to everyone.
Note that to use SCUP you must have an installed, licensed System Center for your business as per the pre-reqs for downloading SCUP.
If you’d like more information about how this all works with some screenshots, post a comment and I’ll put something together.
NOTE: I’ve now created a full guide on how to set this up which you can view by clicking the link below: