So I know that the row in allRows has to come first so I don't repeat the main category like it is doing now. I have been trying for days now to get this right. I can't seem to get it with just if statements and for statements. I need I need to include a function to eliminate excessive iterations, and an if statement so the code doesn't break because of a category with no sub_category. I will also add two more children 'item' and 'options' once i get the first parent/child relationship down. Note: the company ID is just a simple one eventually it will become the true rootNode.
The code below is close to what I want, but still very far. It produces:
Cat1
  subC1 - 1 <--correct
  subC1 - 2 <--correct
Cat2
  subC1 - 1 <--wrong
  subC1 - 2 <--wrong
Cat3
  subC1 - 1 <--wrong
  subC1 - 2 <--wrong
Cat4
  subC1 - 1 <--wrong
  subC1 - 2 <--wrong
Cat1
  subC2 - 1 <--wrong
  subC2 - 2 <--wrong
Cat2
  subC2 - 1 <--correct
  subC2 - 2 <--correct
Cat3
  subC2 - 1 <--wrong
  subC2 - 2 <--wrong
Cat4
  subC2 - 1 <--wrong
  subC2 - 2 <--wrong
Cat1
  subC3 - 1 <--wrong
  subC3 - 2 <--wrong
Cat2
  subC3 - 1 <--wrong
  subC3 - 2 <--wrong
Cat3
  subC3 - 1 <--correct
  subC3 - 2 <--correct
Cat4
  subC3 - 1 <--wrong
  subC3 - 2 <--wrong
Cat1
  subC4 - 1 <--wrong
  subC4 - 2 <--wrong
Cat2
  subC4 - 1 <--wrong
  subC4 - 2 <--wrong
Cat3
  subC4 - 1 <--wrong
  subC4 - 2 <--wrong
Cat4
  subC4 - 1 <--correct
  subC4 - 2 <--correct
I have also been able to achieve
Cat1
Cat2
Cat3
Cat4
  subC4 - 1 <--correct
  subC4 - 2 <--correct
Code
    rootNode   = Node("Categories")
    self.dbCursor.execute("SELECT * FROM Category WHERE company_ID=1")
    allRows = self.dbCursor.fetchall()
    self.dbCursor.execute("SELECT cat_ID from Category WHERE company_ID=1")
    cat_ids = self.dbCursor.fetchall()
    self.dbCursor.execute("SELECT category_ID from Sub_Category")
    sub_ids = self.dbCursor.fetchall()
    for x in cat_ids:
            self.dbCursor.execute("SELECT * FROM Sub_Category WHERE category_ID=(?)",(x))
            subNames = self.dbCursor.fetchall()
            print x
            for row in allRows:
                row = Node(row[2], rootNode)
                for sub in subNames:
                    print sub[1]
                    print x
                    sub = Node(sub[2], row)
This code gets this result.
 rootNode   = Node("Categories")
    self.dbCursor.execute("SELECT * FROM Category WHERE company_ID=1")
    allRows = self.dbCursor.fetchall()
    self.dbCursor.execute("SELECT cat_ID from Category WHERE company_ID=1")
    cat_ids = self.dbCursor.fetchall()
    self.dbCursor.execute("SELECT * from Sub_Category")
    sub_ids = self.dbCursor.fetchall()
    for row in allRows:
        row = Node(row[2], rootNode)
        for sub in sub_ids:
            sub = Node(sub[2], row)
Cat1
  all subcats
Cat2
  all subcats
Cat3
  all subcats
Cat4
  all subcats