Yes, the lower diagram. You want the water entering the panel to be as cold as possible, the larger the temperature difference the more heat is transfered. If the water has already gone through one panel it will be warmer, and thus the second panel in a series hookup will be less efficient. To avoid that you want to have water directly from the pool feed to each panel. This is also good for the reason dschlic1 mentioned, the designed flow rate of the panels is fairly low. You want as much water going through the panels as possible, so every panel should get it's own flow (unless you have a *really* large number of panels).
The panels are intentionally designed to work either way. There are situations where it is impractical to plumb both ends of the panel, so they provide a loopback mode, which makes it possible to make all plumbing connections on one end. That mode is less efficient, but required in rare cases.