While the priest is offering incense, he is actually praying silently the various prayers you can find in a detailed liturgy book, or he is praying out loud. The silent prayers are usually petitions on behalf of the congregation, whether it be asking for God to forgive their sins, or to give them understanding of the readings being read etc.

In Orthodox Christianity, we usually stand to pray to God as a form of respect and to honour Him. Thus, when the priest is offering incense and praying for you, it is nice for you too to stand and to share in the prayer, on your own behalf, as well as on behalf of the priest (fair's fair!).

Once that prayer is finished, we may all sit down (including the priest) to listen to the readings or the sermon.