Yes I think you should be able to recover the x and y components using the real and imaginary parts, that is using MATLAB's real and imag functions as you have suggested.
You can get the magnitude of the acceleration using your expression, Aa = sqrt(Ax^2 + Ay^2) where I assume the Ax and Ay were recovered from the complex values using the real and imaginary parts.
It is simpler though to just use MATLAB's abs command which finds the magnitude of a complex value.
So if the acceleration is given by the complex value Aa you just plot abs(Aa).