In the days of Canadian Airlines, some of the agents could make both types of bookings (ie revenue and award) - so no issues.

I have done this with Air Canada - I have explained the situation - and the Air Canada agent arranged for himself and the Aeroplan agent and I to be on a conference call - so the tickets can be booked at the same time! - subject to availability on a route for both types of bookings!

Of course, if both types of bookings can be done simultaneously online - that would also be useful.