The solution to this puzzle comes from realising that energy and entropy are mathematically equivalent. That is, you can force order onto a previously less ordered body by the input of energy (the work done pushing all the molecules into place, if you like). The fact that entropy increases means that you will always have to put in more energy than the value of the increase in order.

The solution to the "how did we get here" puzzle is that the earth isnt a closed system. Every day the earth is bombarded with energy from the sun. This energy is converted into order through micro-organisms, plants, solar panels, etc. Atheists can explain where we are now using the theory of evolution (provided there has been enough time for the higher life forms to evolve).

Basically the sun's energy powers the earth (and there is always "leakage" or inefficient use of that energy) and that input of energy is why the order on our planet is increasing rather than decreasing