Intel and AMD are both attempting (Or rather AMD is attempting to copy Intel) to use roughly the same set of commands at the machine/assembler levels. Thus the architecture from a software and hardware developer standpoint doesn't matter because the same commands work on both.
This is why SPARC OS, has two versions, one for each architecture that it supports (PC and SPARC). This is also part of the reason why software for MAC OS X won't necessarily run on a linux box, even though they share very similar roots the most basic coding is not compatable. Hence, why Windows doesn't run on a MAC and vice versa, without special software to convert the code over to the other OS.
However, both Windows XP and Linux are designed to run on an the same architecture (I think its x86) that is run by both AMD and Intel. Thus for the most part it shouldn't be a big deal/difference.