For a 20 MHz channel, with 1200 usable subcarriers(18 MHz occupied), what should be the size of the FFT on the transmitter before IFFT is applied? I am trying to simulate the SC-FDMA transmission and I read H Myung's paper and research on the topic but I am not sure exactly on what should be the size of FFT at the transmitter. 

For a 20 MHz channel, with 1200 available subcarriers, what should be the size of the FFT block?

The research talks about IFFT at transmitter sized N = M·Q where Q is the number of users and M is the no. of subcarriers in each block of Q.

So do we perform a M pt. FFT on each Q block or on the entire 1200 symbols at the transmitter before IFFT?

Link to paper: https://ieeexplore.ieee.org/abstract/document/4099344
We perform M point FFT on each Q block, then map the FFT results to intended positions of 1200 available subcarriers (subcarrier mapping), which are finally the input of a 2048-iFFT operation. See the figure below.



Note that this is just one of possible implementations of SC-FDMA which is called DFT spread OFDM. The another is time domain approach. Check this book (Chapter 14) for more details.