To install 12 Cloud Control first thing you need is a database. You can find how to install a 12c database for 12c Cloud Control from my last post. After this crucial step, run the installer for Enterprise Manager as oracle (or any user you wish to use as software owner):

$ unzip -d oem
$ unzip -d oem
$ unzip -d oem
$ cd oem
$ ./runInstaller

As a note, pre-install package for RDBMS 12c sets maximum number of files to 1024. However if you're installing OEM on the same server as its database, you need to increase t to 4096 as a requirement of 12c Cloud Control. Otherwise you may get a failure during prerequisite checks step of installation. To achieve this requirement, as root open /etc/security/limits.conf file and edit the necessary lines as follows:

# oracle-rdbms-server-11gR2-preinstall setting for nofile soft limit is 1024
# oracle   soft   nofile    1024
oracle   soft   nofile    4096

I'll choose to install in Simple mode and keep settings and preferences as default. You can move on with advanced type to customize configuration.

Set database connection parameters.

Run root script

On the summary screen you may find URLs to access Enterprise Manager.

Next step is deploying agents...