Hera does much to hide the ugliness. There are still aspects to editing Ares scenarios that are less pleasant than they could be, but Hera is a very powerful tool.
While you don't need to be a programmer to use Hera, you do need to be patient and technically inclined. ResEdit experience is strongly recommended.
For objects and action sequences, the IDs are arbitrary, and will change if you close the scenario file and re-open it. Objects and action sequences which are created during a session are given temporary IDs from 5000 up; objects and action sequences which are present in the file when it is opened are given temporary IDs from 0 up.
For other kinds of data like conditions and initial objects, within each scenario, each item has an index starting with 0. These indexes are unchaging -- the first item in each list will always be refered to as #0, the second will be #1, and so forth.