Depending on how netCDF was built, you may need to use compiler flags when building your code. For example, many systems build both 32-bit and 64-bit binaries. The GNU C compiler, for example, uses -m32 and -m64 as compiler flags for this purpose.
If netCDF is built with the default compiler flags (i.e. no special flags are used), then no flags need to be used by the user.
If netCDF is built using flags that control architecture or other important aspects of the binary output, then those flags may need to be set by all users as well.