There are many ideas regarding church wide prayer and how it is done. First, it is imperative to have some kind of prayer program for the church; something that unites people in vision and purpose.
Some churches have a set prayer time, a specific time for all the church to come together and pray. Normally a night (or day) of the week is set aside that is not a busy time for church or family matters. Others have a “prayer chain” type prayer focus. This is where people commit to praying a set time; either at church or home. This can be ongoing or for specific period of time. Others set aside specific periods of time to focus the church on prayer. This would be something like “40 days of prayer” etc. Others target specific groups of the church for specific, focused prayer. This would be ladies, me, youth, ministry team etc.
Obviously, everyone should be encouraged to pray on a daily basis and to come pray before each service.