First of all, you are talking about processes that happened *spontaneously*, and the second law of thermodynamics is quite explicit about such processes, they *must* increase (or keep constant) the overall entropy of the universe. Now, I guess your questions would be something like, "How does that happen, because didn't we go from diffuse sub-atomic particles, to atoms, to molecules and planets? That looks like increasing order to me!" Am I correct?
Jrlaguna's response is essentially correct, but allow me to expand on it a bit.
Part of the answer is that those more complex (or more ordered) systems above represent systems with lower potential energy than the ones preceding them. Therefore by conservation of energy, energy must have been released during their formation from the higher energy configurations. A useful (but incomplete) definition of entropy is configurational freedom ... systems with more available configurations have higher entropy than systems with fewer available configurations.
So you are correct that the more complex groupings of matter have lower entropy, because particles that were free to move in any direction before are now constrained to move collectively. Now consider the energy released during the formation of the complex systems ... that energy can be released in many different forms .. such as particles being cast off to carry away kinetic energy, but most likely it is released by different forms of radiation. As Jrlaguna said, because there are so many ways that this radiation can be released, the entropy corresponding to the many configurations of the released energy is more than enough to compensate the decrease in entropy from from the formation of the complex systems.