One day: train and citadel
According to the listing, the excursion with tickets includes hotel pickup, round-trip train, bus and a guide. It is a long day: the listing states 14 to 18 hours in total. Judge it by your children's age and pace.
Two days: Sacred Valley and a night in Aguas Calientes
The 2-day excursion goes through Pisac and Ollantaytambo, continues by train to Aguas Calientes and includes one night with breakfast. It spreads the effort over two days and leaves the citadel for the next morning. According to the listing, one lunch and one dinner are not included, and there is a Cusco Tourist Ticket to pay separately.
Site rules that affect families
The official rules ban baby strollers, backpacks larger than 40 x 35 x 20 cm, food and walking sticks. If you travel with a baby, think about how you will carry them, because strollers are not allowed in.
What to confirm before booking
The listings give no specific rule for children beyond the minimum age, so check the conditions on the listing and ask the operator about the type of train, the hotel and the pickup time.