In practice you can usually consider the APIs to be the same for both ARM and Win32. I.e. the code should compile, link and run the same on both device and emulator.
The main difference between the two APIs are dictated by the fact that x86 is the emulator, and ARM is the device, each of which have subtly different characteristics. However that's no different when considering the .NET APIs, say for networking.
(Naturally there are different paths - these are native binary libraries, so one directory contains the x86 libraries, the other the ARM ones. The library's files will have identical names, so putting them in other directories is an obvious solution)