Is it a requirement that you use Matlab? If not, you could consider my application to solve your general problem: http://bitbucket.org/hexamer/fra4picoscope/wiki/Home
It does require Windows (it's not cross-platform yet). Version 0.4b supports 2204A.
Otherwise, if you need to use Matlab, then I would ask where you are intending to do the phase and magnitude calculations - in the PicoScope app or in Matlab?
There is a math channel formula posted numerous places on this board that computes phase shift within the PicoScope App: acos(integral(A*B)/(sqrt(integral(A*A))*sqrt(integral(B*B))))/Pi*180
If your signals are clean that might work well.
If you're using Matlab, then there are many options for computing phase shift between two signals. One option is to compute DFTs for each signal, then subtract phases. The DFT could be done with FFT, plain (naive) DFT, or Goertzel. Once you're using a DFT, youll get magnitude as well.
If your question is more about importing and manipulating the data, then I'll defer to someone who has more experience there.