The phone line is needed if you have a second subscription as it dials out regularly to confirm both subscriptions remain at the same address (phone number).
You can use what ever pairs in the cat5 you like - If you are making the leads yourself, you can choose.
You only need to use one pair for the box, and this will be on the outer pins of the BT style plug. Put these onto, say, 4+5 of the RJ45.
To make the RJ45 to RJ11, take the RJ45 4+5 pins to the RJ11 - which two pins on the RJ11 alters from device to device, but will either be the inter two, or the outer two. Take a look at the RJ11 socket - it may only have two 'pins' on show.
To test the connection, go to services, setup, and system test.