Right I have started going through the adventures and it would seem that the Skaven could be substituted for the serpent people and the human cultist be dupes of the skaven posing as humans

Skaven dupes would be the Cult of the Yellow Fang. They are given some word-play in Sigmar's Heirs (2nd ed). Their motivation is not "yay we love us some rats." Rather, they see the oncoming end of all things in a pretty depressing light, and realise (for one reason or another) that the Skaven are going to "inherit the world" when it all comes crashing down. So they have decided to throw their lot in with the under-vermin so that they can have a place of "privalege" when the Skaven come to enslave all sentient things. Of course they are going to get no such soft treatment but man-things are so hopeful even when they're being bleak-minded. So the Skaven use these dupes to forward their goals. Also, it is possible that in any given sect of the Cult of the Yellow Fang, that only a few of the higher ranking members would really know who/what they are working for...the rest of them are just dupes of dupes. It gives you a lot of layers to work with in terms of the Skaven involvement of your antagonists.

What he said.

Using the Skaven and layers within layers definitely creates plenty of story opportunities and allows you to expand on them later. I always felt the cult became far too much a charicature of itself in later Freeport offerings. Tying them to the Skaven creates a much deeper consipiracy/evil than they had been given the opportunity to be originally.