Gradebook

Categories are a way of grouping grades so that, if you want, you can weight each category.

For example, your course has the following activities:  Daily activity, homework, tests, exams.

If your teacher does not want to worry about weighting every single activity, you can set up categories so that they are worth a certain percentage of the total.

e.g Daily Activity 20%, Homework 10%, Tests 20% and Exams 50%.

Then, when you create grade items, whether manually or through an activity, you assign it to the specific category.  I recommend to my teachers that they always create an activity instead of just manually adding a grade item as it provides students with notice of the activity and due date etc.  Also, (perhaps this has changed) manually created grade items behave differently in course restore than an activity created grade.

The instructions in the documentation are very clear about how to add a category.  I cannot explain it any better - perhaps if you tell me what about the instructions is confusing you I can help more.

Outcomes are a whole different animal and you don't need to use them in a basic gradebook but can be useful in the right circumstances.  Check the documentation for more detailed info about Outcomes. https://docs.moodle.org/27/en/Outcomes

Scales are a way of changing how the grade (percentage or total points) is represented.  You can create different scales if you want but there is already one set up in Moodle which is sufficient for the majority of users. https://docs.moodle.org/27/en/Scales

The course reset strips all users from the course, and as such, any manually created grade items which attach to the user and not the course (or that is how it used to work but I have actually disabled them for my site so as not to confuse matters).  All grade items attached to activities will remain.  All created categories will remain.

Grade categories are visual and functional. They help you visually order graded items, on yours and the student's grader report. More so, though, they're functional. Unless you have a straight sum-everything-up gradebook, you'll need to break things into categories (folders/groups) to set up aggregation (calculation) methods to control how items are weighted and add up to make the course total (final grade). 

Manual grade items are added directly to the gradebook, and aren't linked to an activity on the course home page. Those grades have to be typed in, manually, into the gradebook. For example, if you're administering a quiz, and it's done the old fashioned way with paper and pencil, you'd need to add a manual grade item to the gradebook in Moodle, and then manually type student's scores into the grid.

"Automatic" grade items are activities, like quizzes and assignments. Those grades are entered directly into the activity, not on the grading grid, and in the case of quizzes (and multiple choice questions) can be "automatically" graded by Moodle. If you manually type a grade for an activity into the grading grid, you override that "auto" functionality and break the link between the gradebook and the activity.

Hope that helps!