Von Mises stresses should not be used for fatigue, since - as mentioned above - you can not see if the stress is compressive or tensile, as Von Mises stresses are always positive values. A common and (in my opinion, the most) simple method is using the Absolute Maximum Principal Stresses (sigma_amps), defined as:
sigma_amps = sigma3 if |sigma3| > |sigma1|, otherwise sigma_amps = sigma1. To be clear, the principal stresses sigma1, sigma2 and sigma3 are numbered in such a way that sigma1 > sigma2 > sigma3.
When you have multi-axial loading and especially non-proportional stresses, the fatigue calculation becomes much more complex when not using specialized software like nCode. When the stresses are non-proportional, the direction of the principal stresses change during the load cycles, which is hard to extract manually from FEA.
A note on the S-N curve: you should always check if the y-axis is in terms of stress amplitude or stress range, as both types of S-N curves are used.