Every combo in the range lands in exactly one made-hand row, so those add up to 100%. The segmented One pair bar is built only from the visible pair rows beneath it, with every segment sized to that row's exact share. Draws and compound-strength rows are counted separately and overlap, because a hand can be top pair and a flush draw at the same time.
The categories describe what your two cards add to the board, not the bare five-card ranking. The board's own pair belongs to everyone at the table, so it never creates or upgrades a category. On 9♦8♣8♦ that means aces are an overpair and deuces are an underpair, rather than both being filed as two pair, which is literally true but tells you nothing. Trips and full houses still need one of your cards in them.
A draw likewise only counts when at least one of your own cards is part of it, otherwise the draw belongs to the board and not to you.
A hand can be in a range at a frequency, and it can be in it on only some of its suits. The two fill a cell in different directions: how often it is played fills from the left, how many of its four suits are kept fills from the bottom. A hand played half the time on two of its suits is therefore the bottom left quarter. Hover a hand and click the corner mark, or double-click it, to pick the suits; the text field takes the same thing written out, as AhKh for a single combo and AJo:40 for a frequency.