To hide any single grade item from students, including Course total:
The line for the grade item you edited should now be grayed out, which lets you know it is hidden. Students will not be able to see it. You can check this by switching to the User view in the drop-down menu in the top of the gradebook, and then in the menus on the right choose a student's report to view and choose to view as "User" instead of the default "Myself," and the hidden item or items should not show. Go back to viewing as "User" to get out of this mode and see the items yourself (but grayed out) again.
By default, Moodle uses a setting called "Exclude Empty Grades." With this setting left as it its, empty grades (from assignments that have not yet been assessed) are excluded from Gradebook calculations and don't count against students. If the Exclude Empty Grades setting is de-selected, empty grades are calculated as "0" and your students may be alarmed by low course totals early in the semester.
The extra credit box is used to indicate that the entire item is extra credit points, above and beyond the regular point total. This kind of grade item is meant to be used alongside another, non-extra-credit grade item that represents the "normal" points that you can also earn in that category. You can then make the extra credit item equal to the amount of extra credit points that you'd like to grant.
You can also exclude the lowest grades for a given category in the category settings page.