Exit/Entry system with a layover in a Schengen area country?

Hi all,

US citizen first time traveling to Europe since the Exit/Entry system.

I am trying to book a flight from Brussels, Belgium to Marrakech, Morocco and I’m seeing flights with layovers in other Schengen area countries.

Will I have only the exit system in Brussels or also go through it during my layover?

I’ll also be going back to Portugal afterwards, will the re-entry system be quicker/smoother?

TIA~