There is no substantial differences when using FFTW wrapper or use FFT directly in MKL.
FFTW is from www.fftw.org, it is third party FFT package, which have itself function name rule and data definition (include source code implementation). for example
** Create FFTW plan for 1D double/single precision forward transform
my_plan = fftw_create_plan(n, FFTW_FORWARD, FFTW_ESTIMATE | FFTW_IN_PLACE);
** Compute DFT
fftw_one(my_plan, x_in, NULL);
The FFTW wrapper in MKL is just for the developers who used to use FFTW interface to write FFT code and also can use MKL FFT at the same time. The wrapper is the bridge of FFTW interface and MKL FFT implementation.
MKL support FFTW wrapper since 7.0 and these wrappers enable using Intel MKL Fourier transforms to improve the performance of programs that use FFTW without changing the program source code.
You may see some detials in MKL user guide and Appendix F: Appendix F: FFTW Interface to Intel® Math Kernel Library