Prepare data for FFT
If you're using the usual Decimation-In-Time Cooley-Tukey radix-2 FFT, the buffer of samples going in need to be scrambled in order by having the indices of the samples bit-reversed.  And if the FFT is a complex-input, complex-output FFT and it is given real data, yes the imaginary part is set to zero.

And, in the case of a purely real input signal, you need not bother swapping those imaginary parts in your data preparation before passing to the net FFT algorithm expecting the input to be in bit-reversed order.  But you do have to bother with the real parts of the samples.