You need to understand the architecture, then it'll make sense. Read p. 9, then start on p. 43 in the manual.
A preset is the modeler's equivalent of a full amp rig with a pedal board and the pedals wired in whatever order you set up but that wiring is fixed for the duration while you use that preset. There can be up to 8 scenes stored in a preset.
The Scenes bundle the settings for each block; each scene remembers the currently active channels and bypass states for each block. In the analog world of the effects on a pedalboard, it'd be like having all your effect pedal settings and their bypass state stored in an 8-scene effect switcher with the wiring that you defined AND the ability to change effects to a different model of that type. So a Wah block will always be a wah, but it could be one of many brands or models, the same is true of almost every other block, with a couple exceptions.
Blocks, for the most part, have four channels, each of which is just the settings for the block,
and the block's type.
Saving the entire preset saves the state of all scenes, which already contain all the block information. Being able to save an individual block's changes would require having separate setting files for every block in every scene in every preset, which would be unmanageable. That said though, we have the Block Library, which allows us to save a particular block for later reuse. That doesn't update or change the preset or scene, it's a separate mechanism which allows us to save the entire block, or just the current channel for reuse in any other presets simply by adding that effect block to the grid then selecting the saved block from the library.
It took a couple attempts to get my head wrapped around it because I bounced off several other brands' modelers, but once I did I like it much more. It's flexible and makes sense in light of it acting like a virtual pedal-board.
