Firstly, you will need to connect the LOC by the amp in the hatch. A few things to remember is you need to be absolutely certain that you can tap the line outs from the amp. If you accidentally tap the line ins then the signal will be so low that you'll barely get anything from the speakers and you will have no sound output at all.
Secondly, you will also need to do two things to get the LOC up and running. Either you tap the stock head unit power wire or the amp's power wire in order to power the LOC. Or if this does not work then you might need to tap the amp since it is right there.
Please ensure you find a wiring diagram for the relevant amp, so that you're tapping the proper wires. For the signal, you'll be required to tap the R & L speaker outputs from the amp, and power for the other. Be advised, though: You need to find out which amp goes with which wiring diagram.
If you're also adding the LOC to be able to add a sub, you should first discover if there is any built in crossover or filtering going on in the amp. If there is, it might be filtering out the sub bass frequencies in order to protect the stock speakers. This would result in making your Line Output Connector useless for adding a sub. Another useful site for more details is vwvortex.com.