If the box is just for Tivo use, then it wouldn't be too hard to optically shield it from IR signals from the remote & vice versa - stick the TIVO emitter (via IRDA adapter or Red-Eye if it's an IRDA STB) to the front, with foil tape to shield the IR sensor.
If you want 2 STBs responding independently to 2 different remotes, then it can't be done with either of NTL's remote systems - IRDA (1000,1010,2000,4000 STB) or RC5 (4001), as there is no a/b code switching (as used on many VCRs) supported.
For IRDA boxes, it could be done using either
A Red-Eye Translator plus some foil tape to shield the STB's IR receiver from IR from the IRDA remote, or for the 'ultimate' method, a Red-Eye on each STB - Red-Eye supports two A/B code sets and so two of them can respond independently to two remotes.