I recently booked travel using MR points for partial payment.

You book travel on the AMEX site (I booked on United). Elect to pay all or some using MR points.
The full amount is charged to your AMEX card (I noticed that the amount charged by AMEX was slightly higher than buying the tickets from the airline due to AMEX service charge applied)
You receive a statement credit for the value of points used. In my case I bought $1000 worth of tickets, used 87k points for $877 credit. The charge and credit show on the same statement so you shouldn't be at risk of them appearing on different statements.
My flight was immediately booked on UA's site, so I was able to go there and pick my seats and e+ for my family (I have UA status)
I received 17k MR points back from AMEX representing 20%, so net MR usage was 70k for the $877 credit!
I received full EQM/EQS credit for the flights/miles travelled on United (since they were purchased tickets.)

The exchange value using MR for flights was so much better than using them for hotels, etc. I was very pleased with the experience! And United was asking 50k/ticket so it would have cost me 200,000 UA miles for the 4 tickets.