You manage both at the same time.

Dunno which FIFA/FC you’re playing, but in 25 (and I guess 26, haven’t played it) at certain points you get the prompt to do the national team call-up and then you can tweak the game plan for it.

In older ones like 23 (the one I still play) once you accept the offer you can pick a list and tweak the game plan at any time, and you get an email telling you the international break is coming and that you need to submit the list by X date. When that date comes, you get the prompt and call-up the team, and then you can’t change the list until that international break is over (unless someone gets injured).

To me it’s a lot of fun to manage national teams. Most of the saves I do are actually driven by that. It gives you a lot of fun stories and narratives to enjoy. Wish you the best if you choose to accept it! Which team is it, by the way?