I went through this when mine were 1 and 3, very close. I did clearly explain the new agreement with my 3 year old. It was hard for me to leave the 1 year old as he was very much a momma’s boy at the time, so my ex and my older boy got some alone time in the beginning. But once my little one got over the separation anxiety phase he seemed to take to our new situation just fine. Having his older brother around helped a lot I’m sure.
Tell them, but make it exciting! Ask them “Are you excited to go see Daddy!?” Give them special toys to keep there so they will look forward to seeing them. Pack their clothes in super cute/cool suitcases for the back n forth. Make it as exciting as you can.