Oh no!! So sorry the rules were confusing! The goal is to sort the stacks of cards on both sides by suit into the 4 piles at the top similarly to how Klondike solitaire works. The alternating colors stacking rule only applies for the piles of cards on the side since those are the piles youre organizing to uncover the cards so they can be stacked at the top.
So like if the hearts stack on the top had a 3, it would need a 4 of hearts, then a 5 and so on. Cards will automatically move themselves to the top when they can be moved there so you only need to worry about organizing the two tables. Hope this helps! Again, sorry it was confusing :(