The way the skeleton files in the v2.6 SDK are arranged, the platform-specific stuff goes in Makefile.osx, Makefile.linux etc and the platform-independent stuff goes into Makefile.inc, which is included by the other Makefiles.
In most cases, any header and object files you add are going to be needed regardless of platform, and so should go in Makefile.inc. There are variables PLUGIN_SOURCES and PLUGIN_HEADERS near the top that can be extended with further headers and .c/.cpp files (the .o files will be deduced from the .c/.cpp names) or you can add .o files directly to PLUGIN_OBJECTS further down.
I hope that addresses your question!