As far as I know there is no 'A/B' code capability in the NTL IRDA remote system, to allow 2 remotes to control 2 STBs independently. There is a colour coding system but this is for multiplayer games, and every colour will operate both STBs.
NTL could in principle have an 'only respond to remote colour x' user-settable option, but I think this is one of the many desirable software improvements I doubt we'll ever see happen.
However, if you are using Red-Eye on one STB, then as long as you can shield that STB from the IRDA remote, then you can have independent control of the STBs - one from the Red-Eye compatible remote, and one from the original NTL one.
The STB will need quite a lot of shielding as the IRDA remote is rather powerful. I would recommend using some aluminium foil tape (paper is surprisingly transparent to infra-red) over the left-hand side of the STB window, covering the area from the left side to the first digit, and to the full height of the window. You need to make a small hole (3mm) in the tape, near the STB's IR Receiver (shine a torch into the window to see where it is), and place the Red-Eye so that its emitter is over this hole.
If you really want to cut remotes to a minimum, you could place one Red-Eye on each STB. Red-Eye does support dual code sets - it will 'learn' which code to use by the first code it sees after switch-on. See the question "I have a Philips DTX6370/1 receiver...." on page
www.redremote.co.uk/faqs.html for more details. Pronto CCF files for both codesets are available.