I'm confused about how organelles communicate with each other. I understand signaling between cells and the whole transcription and translation of DNA process. However, how does a motor protein know the destination of its package? How does a lysosome know when to break down a worn out organelle? How does the cell distribute ATP to the organelles where it's needed (how does it figure out where the ATP is needed?)?
There's no single common mechanism for intracellular communication, and some of the mechanisms (and some parts of some of the mechanisms) are known in much greater detail than other. For each of the processes you mention, we at least know that they proceed via very different mechanisms.
ATP distribution, for example, proceeds mostly by simple diffusion. ATP is a small molecule and is able to diffuse fast enough that it can move from one end of a cell to another in about ~20 ms on average .
Our picture of how ATP actually gets taken up by the various organelles is much murkier. For the case of the endoplasmic reticulum (ER), there is evidence that ATP is brought in via an ATP/ADP antiporter . Transporting ATP via an ATP/ADP antiporter would have the effect of keeping the ratio of ATP/ADP stable in both the cytosol and the ER. It is reasonable to assume that similar mechanisms control ATP transport across other organelle membranes, but you'd have to dig into the literature to find out details.
1: Diffusion coefficients of ATP and creatine phosphate in isolated muscle: pulsed gradient 31P NMR of small biological samples
2: Transport and transporters in the endoplasmic reticulum