Best way to pass custom order totals to Checkout

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So I have two apps installed that both update pricing in the cart and neither of the developers have been helpful with getting the two of them working together so i am hacking away.

The Apps are Bundle Builder and Wholesale Pricing Builder. Both have their own math functions so I was able to assign a few variables and get all the pricing working on the cart page but I am having some issues passing those values to the checkout.

Does anyone know of a good tutorial that covers passing custom values to the checkout besides the checkout object doc: 

Or does anyone want to help figure this one out? Just looking for a push in the right direction.