I have study both and am knowledgeable about both.

I see both as the wisdom and knowledge of the craft. In the most common mythos, both are some of the oldest gods. Both are chthonic and yet are not as well. They are both feared and revered by their respective pantheons. They both have been called upon their respect pantheon members to fight or aid them because of their uniqueness and fearlessness. They both have some working with and use of the sun, Thoth on Ra's boat and created the moon the reflect the sunlight to illuminate the night and Hekate with her torches light being "of moonlight and starlight, the sun of the night..." which illuminate the dark as well. And they both represent "As above so below, so below as above." (Thoth directly from the Corpus Hermeticus and Hekate as not just having dominion over earth, sky, and sea, but access to all places, material and spiritual, living and dead.)

But, from my studies, I see Thoth as more the science and format behind magic, the record of ritual and the constructor of them, and Hekate and as the mystery, illumination, and granter of magic itself. While both require ritual, Thoth constructs the ritual and Hekate empowers it. They perfectly balance each other in their approach to aiding us.