Alloy isn't just a plug-in, but instead a system of effects. Sometimes you'll want to load an entire preset (update the whole system), but other times you might just want to use parts of a preset - e.g. just change the Equalizer settings. Selective loading of modules gives you this option.
When you select a preset from the list, the settings of any modules which are checked are being taken from the preset you selected.
You can change which modules a preset loads by selecting the preset, then clicking on the checkboxes. So for example, if you want to load a particular presets Equalizer settings, un-check all of the modules except for the EQ checkbox, and only the Equalizer module settings will be loaded.
Each preset remembers which of its checkboxes are checked. As soon as you click on a checkbox, this change will be saved to the preset.
Note: There is a shortcut to quickly check just one module. Hold the Alt key and click on a checkbox, and it will be selected while all others are deselected.