Hi Wayne,
AequilibraE 0.6.x for QGIS has a facility to import matrices from "layers", which allows you to import matrices from text files loaded in QGIS as ORIGIN,DESTINATION,FLOW
If you want to create from NumPy, you need to remember that NumPy is base 0, so you would need to shift your matrix by one in both rows and columns, but you will probably have trouble assigning it. You can go around it by having a dummy centroid 0, but I am not sure that will work.
I am currently working on the next version of AequilibraE for QGIS, and might consider improving the import of matrices.
You can also do it directly in Python (I haven't tested)
from aequilibrae.matrix import AequilibraeMatrix
mat = AequilibraeMatrix()
mat.create_empty(file_name='D:/my_matrix.aem', zones=52, matrix_names=['matrix1', 'matrix2'])
# Sets the index to be from 1 to 52
mat.index[:] = (np.arange(52).astype(np.uint64) +1)[:]
# Fills the first matrix with ones
mat.matrix1.fill(1)
# Fills the second matrix with an identity matrix
mat.matrix2[:,:] = np.eye(52)[:,:]
mat.close()
Pedro