Agree -
Positive to Positive, negative to negative in theory; in practice, it ends up being negatives routed to ground (ie, frame), postive on one battery to the postive on the other, then one positive routed to the starter.
Here's what it looks like in the trunk of my Chevelle:
Negatives are to the rear, and you can see them poking through the trunk floor headin' to the frame.
The positives are the forward post, and you can see the cable (inside the convoluted conduit) running across the rear of the trunk and through the latch area.
The side post/top post batteries make it a little easier, since it provides a place for all this stuff to hook up to.
Lastly, everything goes through that Moroso master cut off switch before heading to the rest of the car.
K