Can I book my ticket on one passport and have visa on other?

Do they check visa in passport i gave the number? I have to citizenships, and on my German passport I will have the visa (Im still waiting 6 weeks for the passport and don't know the number), however the ticket I will buy on my polish passport (now), of course both of them I will take with me. Do they only check the number or visa as well? I will be going between beijing and shanghai.