Yes it is allowed to install EM 12c on same host but you need to make sure that the hardware is strong enough to keep both the OMS’es up and running. For production system setup i will not recommend you this approach but if this if for your testing purpose you can install both the OMSes on same host with different repositories.
Your second question is not clear, if your final goal is to have em 12c in your enviro then you can go through the proper EM upgrade method which will take care of all target and history migration. Manually doing all is not supported.
Pls go through this: http://download.oracle.com/docs/cd/E24628_01/index.htm
If you decide to install both 11g and 12c on the same machine, remember that the OHS server administration port is by default common for both - 9999. There is no option to customise this during the WLS installation itself.
So, webtier in the 12c install will fail to startup if the 11g oms is running.
To modify the port in the 11g OMS:
- Stop the oms :
emctl stop oms -all
- Take a backup of the <gc_inst>/WebTierIH1/config/OHS/ohs1/admin.conf
- Edit the file and modify the port 9999 references to some other free port. Save the file.
- Re-start the OMS.