Once all the boys arrive, then you can proceed with den meeting as usual. We like to have our Denner assign a boy to offer a prayer, assign another boy to lead us in the pledge/flag ceremony, and assign another to lead us in reciting the scout law, oath, sign, handshake etc (ideally we do one or two at the beginning of den meeting and one or two at the end).
In our den we say the prayer first, this way it shows the boys that God comes first in our lives before country (the pledge) and den (the scout law etc).