The history of the founding of Rome is the stories of their gods and goddesses. You can’t get around it. Now, as you move further past it’s founding time period, you’ll move further away from some of the more constant referencing to them and into the actions of the Roman Republic and then the Empire.
My children have never been confused, but I intentionally chose to stay with American history, with just a few of the ancient and most important tales for familiarity but not study, until they were around 9, when we began in the Middle ages and then started the Ancients finally when they were 10/11. I wanted them to have a strong foundation in the One G-D before we dug in deeply into the others who were made by man and those supernatural creations desiring worship for themselves.
Additionally, I have always taught that G-D has never claimed that He is the only supernatural entity, just that He Alone is G-d and who deserves worship. He doesn’t deny that there aren’t other created entities vying for our worship – quite the opposite.
Though we do not accept the accounts as factual, the ancients did and real people did settle in the ancient world. Plus, remember that there was rampant ancestor worship then and I always taught, too that it’s very likely that the founders of these great civilizations transformed their ancestors into “gods and goddesses”, since they worshiped them anyway. So if you keep it within the context of the time, it’s not complicated, it’s just a matter of communicating it to children. They will read for themselves in the Bible that G-D didn’t deny the presence of other entities in the world, so to deny that they existed at all will come into conflict with what the Bible actually says.
I hope I’ve made sense. it’s late, thought I knw what I’m trying to convey to you. It’s a vastly interesting topic and usually one downplayed, but it’s not simplisitic either and makes some people uncomfortable.