I can't tell you the best way, but I can tell you "my way"... and what I find works best for me...
Let's say I've created a bunch of ES2 synth presets.
I like to save them in folders:
e.g. 'My ES2' will be the root folder.
Within this folder will be sub folders:
01 Synth Bass
02 Electro Pads
03 Electro Sequences
04 Ambient Pads
05 Ambient sequences
I use a similar folder system for channel strip settings.
You can create your folder structure for presets (for say the ES2) in the Finder in:
Your User / Library / Application Support / Logic / Plugin settings / ES2 /
or when you're saving presets or channel strip settings:
Click on the preset menu for the plugin and choose to save setting as..:
Then, choose "New Folder" or use the OSX shortcut (CMD+Shift+N)