Jad,
When a policy package is installed, the FortiManager's task is to ensure that the resulting policies on FortiGate exactly match what is outlined in that package. In other words, packages are not additive.
It is dangerous to have a FortiGate as an installation target for more than 1 policy package at a time because of the potential for human error in installing the wrong policy package (though FortiManager does give a warning if an admin user tries to push a policy package different than the one previously pushed).
It is for this reason that the FortiManager Best Practices Guide states:
"Each managed device should only have one policy package associated with it. This will help to ensure that the wrong policy package is not mistakingly installed to a FortiGate."