The underlying theory of quark-interaction is QCD, that was before Yukawas theory of meson exchange interaction. Yukawas theory could explain some features of the nucleon-nucleon interaction, but not satisfactory.
However, there are many problems how to go from QCD to Forces between hadrons.
i) Coupling constant of QCD becomes so large in the energies you have in hadron physics so you can't do a perturbative expansion in terms of the coupling constant of QCD (just as you would do in QED and in high energy QCD).
ii) The force between quarks are due to their colour charges, but hadrons are colourless..
However, effective field theories have been developed the last 20years or so, the most famous is Chiral Perturbation Theory.
Just because we know the theory of electrons and atoms, doesn't mean that we understand the behavior and properties of solids. The same analogy holds here too.
This is the best link I can give you to Forces between hadrons as explained by Chiral Perturbation theory:
http://arxiv.org/PS_cache/hep-ph/pdf/0210/0210398v1.pdf ( I study that document myself, are doing my master thesis in hadron physics)
But you might want to start to read this short guy first:
http://en.wikipedia.org/wiki/Chiral_perturbation_theory :-)