That's it. Now every element in that array is also an array which contains the actor ID and a value: [ID, value]. But think about this, you don't need arrays again because the position in the array @love_pts will serve as the actor ID, right? So @love_pts[ID] = value would do just fine.
So instead of your @love_pts array looking like this:
[ [ID1, value1], [ID2, value2], [ID3, value3] ]
it would look like this:
[ dummy value (because actor ID with 0 doesn't exist), value1, value2, value3 ]
You can just refer to the array like this. Say you need to access the affinity level Arshes ( ID 1 ) has towards Gloria ( ID 8 ).
$game_party.actors[0].love_pts[8]
"$game_party.actors[0]" is Arshes, and ".love_pts[8]" is his affinity level towards Gloria.
I hope I was not too confusing...