Usually you do not need to normalize the fields since it is automatically normalized: https://optics.ansys.com/hc/en-us/articles/360034405254-overlap-Script-command you can mutiply a factor to one mode the result will not change.
If you simply want to compare the fields, you can normalize each field, but care should be taken that both E and H fields keep the same relation.eg, if you normalize E to be max 1 V/m, the H field cannot be normalized to be A/m in Physics. However in the case of overlap you can do such normalization since the result will not change.
You can also write your own script to calculate the overlap, which is straightforward.
 As for the similarity, since it only counts the tangetial components, if you compare the whole intensity it might not be obvious. Please only compare the tangential field components. Do not involve the axial component.
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