The answer to this question is No.
Seems existing bookings (which are in credit) or gift vouchers cannot be used in the Business Direct portal. Something to do with the Booking Office that is assigned to the existing booking shell, even if the ABN (of the Aquire account and the Business Direct account) is already in the booking.
Not very happy about this: they have increased the price of public tickets to offset the discount possible via Business Direct. E.g. SYD-BNE Flex fare booked on 25-June was $388.99, now $395. So now that they already have my money in existing credits and vouchers, they are going to gouge even more due to the at least 2 or 3 price increases in the last 9 months, with no way to take advantage of the Business Direct discount.
November last year, Flexi CNS-BNE was $267. That's now jumped to $285 on the public site and is still $273 via Business Direct.
Also, the 5% discount on Flex Domestic is a bit of a furphy:
SYD-BNE-CNS Flex is $335 on public site, and $321 on Business Direct. Last time I did maths, 95% of $335 was $318.25. And while they will claim the caveat that the discount is on base fares, considering Qantas *never* show the breakdown of fares, unlike VA, they really could get away with anything in that regard. Surely there's something to do with false and misleading advertisement in that somehow...? They've got to publish the base fares before they can claim that people will save 5% or 10%, surely?
It's all show-and-tell and nothing which substantially helps Small Business... just more marketing and advertising. C'mon Qantas, you can do a better job than this.
Okay, bit of an update after my little rant here...
Received an unexpected message from Red Roo, and then a phone call from the Premium Service Desk about this. They have been able to update their procedures, and, as I understand it, existing Credit Vouchers and Gift Vouchers can be used to book Aquire discount fares, but they have to be done over the phone through the Qantas Reservation Call Centre (e.g. the Premium Desk for WPs etc., as opposed to the Business Direct number - details are a little sketchy). I think they also mentioned multiple vouchers could be used on a single booking (In my previous experience, this has been up to four vouchers).
After receiving the previous information, and having resigned myself to not being able to use the vouchers to receive the discount, I had already booked some flights. The operator in the Premium Service Desk took the details of the bookings, and has re-processed them and I've received a refund on the price difference. A very good outcome, I believe.
The fares are still M class, but the fare conditions have changed from MQFLEX to MQUA.
I asked if there was a way for others to be able to point operators to the correct procedures (e.g. a Right-on-Q number), but I guess they've learnt the lesson from giving those numbers out (e.g. for bookings MASAs), and was told operators could look up the Qantas Business Direct procedure to get the correct details.
Overall, I'm happy for the outcome, and once again, am thankful for Red Roo's involvement in this forum: while I'm not across the detail of their internal workings, it appears they were able to highlight the gap in this process, and have helped QF come up a with a positive solution for the customer.
As always in these instances, YMMY, but good luck all the same.