Not a beginner question at all. Scoring questions, although not the sole responsibilty of the umpire, often dominate this topic. Scoring rules are found in the Official Baseball Rules.
In your question, the batter is credited for how he got on base (hit, walk, HBP) and any pinch/courtesy runner would get credit for any further action.
In HS scoring, the credit for scoring a run may or may not be entered in and more likely not entered in correctly. But the OBR does have it specified in the rules. I have included the rule for your reference.
Hope this helps......
Official Baseball Rules 10.02
The official score report prescribed by the league president shall make provisions for entering the information listed below, in a form convenient for the compilation of permanent statistical records: (a) The following records for each batter and runner: (1) Number of times he batted, except that no time at bat shall be charged against a player when (i) He hits a sacrifice bunt or sacrifice fly (ii) He is awarded first base on four called balls (iii) He is hit by a pitched ball (iv) He is awarded first base because of interference or obstruction. (2) Number of runs scored