Resources are divided into two categories, the viewing of which can be switched between by clicking the JavaScripts / StyleSheets button in the open manager.
Including or Excluding Resources
The managed resources of either category (JS or CSS) are displayed in an intuitive split panel - Green for those we want to use, and Red for those we don't.
When the user visits any JavaScript or CSS resource page, the manager will show an extra button marked Manage this. By clicking this button, we will open the manager, and if the resource is already managed, it will be highlighted. If the resource is not already managed, it will be added to the red section. To keep the resource under management, simply Save the configuration.
Users can also add resources by typing or pasting the full title (e.g. User:Example/someScript.js) into the manager's included text input and submitting by pressing ↵ Enter. In this case, the resource will also be added to the red section, and again, to maintain the configuration, click Save.
To manage the resources, just open the manager, and drag resources from red to green, or vise-versa to activate or deactivate that resource, then Save the changes. If any resources are newly activated when the new configuration is saved, they'll be immediately added to the page. All the resources in the green sections (of JS and CSS) will be included on every page visit from then on (until changed).
The resources will be included in the order they are displayed in the manager, so we have full control over how our resources are loaded.
To remove a resource from management, simply drag it to the bin icon, drop it in and Save. Before saving, anything added to the bin can be reinstated by clicking the bin icon to open it, and dragging the resource(s) back into the manager's red or green sections.
The manager will close automatically after clicking Save, or can be closed explicitly by clicking User Resources or Close.
Purging the Session Cache
The option to Purge the session cache will initialize a fresh request for your managed resources on the next Wikipedia page load, by wiping the related sessionStorage. On the next page load, the session cache will be rebuilt, and used thereafter. This functionality is included for technical reasons which boil down simply to rebooting.
Temporary Inclusion
Managed resources in the red sections can be loaded temporarily at any time without changing the configuration, by clicking the resource name. A browser dialog will show asking if you're sure (just in case your click was an accident), and if confirmed, the resource will be loaded - just that one time.
This allows infrequently used resources to be included on demand quickly and easily without any editing, dragging and dropping, saving or changing the configuration in any way.
Resource Link
Each resource is appended with a link to its page.
Especially when using resources developed by other users, it is advisable to add the resource to your watchlist, and familiarise yourself with the code. If the resource is changed, you'll want to be aware of how that affects you as a user.
Also, if the resource isn't working properly, or you want to ask the developer to add a feature or have any other questions, you may want to visit the resource's talk page.