I have not tried this but you could try:

Put on your $5 at $1000 as "Market on close". Make your amendment in a separate bet through the API to $6 at $1000. You now have your 2 bets so cancel your first bet leaving you your $1 at $1000.

As I said I have not tried this but I would have thought this would work.

http://bdp.betfair.com/docs/PlaceBets.html