In the November 10th, 2013 issue of The Lookout Magazine they give 4 ways in which to pray for missionaries.
1. Get a list of the people your church supports.
2. Make a daily, weekly, monthly schedule so you have time to pray for each one listed.
3. List topics you want to address when you pray for each:
Their family: pray for their marriage, pray for their children by name.
Health: pray for protection and rest.
Ministry: find out specific activities they're involved with or need they have.
Their field: pray for the unique challenges of the pace where they live and work.
4. Send the missionaries a note after you've prayed for them.