If you're not writing something which compiles its own tools which are then used for the rest of the build, or is not a compiled programming language, all you have to do is respect the CC, CFLAGS, LDFLAGS and LDLIBS variables coming from the distro. Then you will use the correct cross toolchain and libs.

If you need to compile programs that run on the build machine, you should have a ./configure script which allows a host CC and target CC to be specified, and use them accordingly. Even if you deviate a bit from what others are doing, if it is clearly documented and working, the downstream package maintainer can handle it.