Preamble: I'm writing this blog from my iPhone in the hopes of getting this out quickly before I forget. Please pardon the lack of screenshots or a step by step due to the limitation of the mobile blogger platform.
Fusion Middleware 11g provides the ability to manage its components such as Oracle Identity Manager via Fusion Middleware Control. However if you have multiple Fusion Middleware deployments and Enterprise Manager 12c you can use the latter to centralize and simplify management of your environments.
Enterprise Manager 12c uses a feature called auto-discovery to discover and add targets. Once auto-discovery is set up you can view the discovered targets and 'promote' the ones you want to manage. This enables you to quickly add your database targets which includes Grid Infrastructure, listeners ASM and the database instances out of the box. However an extra step is required for your Fusion Middleware targets. Auto-discovery has to be explicitly configured for FMW. The documentation describes the steps here http://download.oracle.com/docs/cd/E24628_01/install.121/e24215/fmw_discovery.htm
Once that is configured any new FMW are automatically discovered and you just need to promote them in order to manage them in Enterprise Manager 12c.
Of course you can always manually add the targets but where's the fun in that?