The text is from Chapter 5 of Joseph Glanvill's Scepsis Scientifica: Or, Confest Ignorance, the Way to Science; in an Essay of the Vanity of Dogmatizing, and Confident Opinion. The subtitle of that chapter reads: "We can give no account of the manner of Sensation." It is to this form of ignorance that Glanvill will turn his attention.
Here is the text without ellipses (page 26-7):
Besides, how is it, and by what Art doth it read that such an image or stroke in matter (whether that of her vehicle, or of the Brain, the case is the same) signifies such an object? Did we learn an Alphabet in our Embryo-state? And how comes it to pass, that we are not aware of any such congenite apprehensions? We know what we know; but do we know any more? That by diversity of motions we should spell out figures, distances, magnitudes, colours, things not resembled by them; to some secret deduction.
Note that the word "congenite" is obsolete for "congenital". The "it" refers to the "Soul" mentioned in the previous paragraph. He wants to show that we do not know how our sensations, that is, what we experience, mean what they do to us.
Here is one possible paraphrase:
Besides, how is it possible and by what means does the Soul read an image or stroke in matter (whether that be of her doing or of the Brain, the problem is the same) to signify such an object? Did we learn this in the embryo state? And why are we not aware of these congenital teachings? We know what we know, but do we know any more? By what secret deduction do these diversity of motions allow us to spell out figures, distances, magnitudes, colors, things not resembling them?
"congenite", Wiktionary https://en.wiktionary.org/wiki/congenite
Glanvill, J. 1885 Scepsis Scientifica: Or, Confest Ignorance, the Way to Science; in an Essay of the Vanity of Dogmatizing, and Confident Opinion. Kegan Paul, Trench & Co. (Internet Archive: https://archive.org/details/scepsisscientifi00glaniala)