You can't really help it the way they designed it. You would have to be 75 to realistically finish Zilart. Meanwhile, you can get started on CoP missions at around 30.

The lapse of the two stories is tiny an inconsequencial. CoPs story line is just confusing early on period whether or not you've finished Zilart. The fact that most go months between missions makes it harder to get a flow of events clear in your head.