Having both modules is a logistic headache because both have an "add to cart" command, both have "view cart", and the two carts have different options, layouts etc - so your customers aren't going to know which is which. And nor are you, when you start to get the confused emails asking what's going on; assuming that your customers don't give up and go somewhere else first.
But what you want to do is trivial with checkout and checkoutdownload: have two products, one free and one with a price. The free one has associated with it (via checkoutdownload) the small download size, the priced product has the larger download. Presto hey.