Custom Bins simply store shortcuts to presets.
Preset Bins actually store the presets.
I mean, they’re both containers for data stored elsewhere, but this is how they function within the Premiere interface: one holds links, the other holds the actual presets.
Thus, Custom Bins allow you to organize presets while leaving them in their original location, which is useful when setting up a bin for commonly used presets.
Preset Bins are great for holding presets that are project specific. For instance, I’m currently working on a project with some pretty bizarre color balance and level settings. It’s not likely that I’ll ever use them on another project, so I’ve set up a Preset Bin named with the title of the project.
On the other hand, I use things like Cross Dissolve, Reverb, Brightness/Contrast, Colorista, and Exponential Fade in most of my projects. Thus, I’ve set up a Custom Bin named “COMMON” with those effects in it.
And now you know.