RTI stuff all works together much better when all the remotes and processors or in one file. I have noticed that if you have two or more systems in a home that are not tied together as a single file system, and that even when you are using different master code numbers, the number of misses and errors you will get is dramaticaly worse than if you kept all the processors and remotes in one single file and simply addressed remotes to the individul procesors & ports.

If you are worried about IR confilict, then you need to focus your designs around system macros and port addressing. I have systems with as many as 11 remotes, multiple touch screens and 4 plus RP-6 processors all of which can be rather busy at times, with little or no IR conflict issues Simply because everything is based upon port addressed system macros