Hi,
Select one of these two packages as the master package. In this package you have to do two things:
1. Go to the "Installation targets" and add both fortigates as targets (one FG should be already a target).
2. Go to "Objects configurations" and make interface mappings for all interfaces engaged in policies for both FGs. An interface mapping should be like:
FMG interface object A <-> FG-1 interface X
FMG interface object A <-> FG-2 interface Y
FMG interface object B <-> FG-1 interface XX
FMG interface object B <-> FG-2 interface YY
and so on...
(2b. You might also need address objects mappings or other mappings as well, for example if one address object has different value in one FG than the other).
When you finish with all this, you'll have a single policy package with both FGs as installation targets and interface mappings for all interfaces of all FGs. Any change you make in this policy package during installation will be installed to both FGs.
You must remember this: Having a single policy package for many FGs is a very good practice, but you need to keep an order in many things: like the naming convention, in maintaining a common policy for all FGs, in the addressing, etc. If you cannot maintain this order, then you'll end up with a complex and impossible to manage policy package.
Cheers