It's pretty simple really. First you need to write out your plaintext and count the frequency of each of the letters in the plaintext.

Now choose a set of 40+ symbols to do the homophonic substitution. You randomly assign these to the letters A-Z making sure you assign more to the letters that you use the most in your plaintext (probably e and t having the most)

Now decide on an arrangement of the plaintext (transposition cipher), this may involve writing diagonally or spirally or in any pattern that can be conveyed as a key and is easy to write out.

Finally, substitute the symbols, where you have a choice of more than one symbol pick one randomly. This should be done randomly rather than methodically to make the cipher the toughest to decrypt, you could use dice to do this.

The decryption key that you pass to anyone wanting to decrypt the ciphertext is the set of symbol substitutions and the way that you have transposed the symbols. (E.g. spiral going clockwise from top right)

I've seen speculation that his method may have been as simple as the ancient Spartan Scytale (https://en.wikipedia.org/wiki/Scytale).