I think you ought to know I'm feeling very depressed.
I couldn't find anything in the rules that explained what happens when the Well cards run out.
I would have thought that the Ruins got shuffled to form a new deck but you need the Ruins for many of the cards abilities.
In the end we left about a dozen cards in the Ruins and shuffled the rest into a new Well.
Karmaka Rules pg. 11 wrote:
If a player needs to draw or look at a card from the Well, and the Well is empty, shuffle the cards in the Ruins (except the top 3 cards, which remain in the Ruins) into a new Well; then proceed to draw cards as needed.