In series, you will only need to run one pair of wires from the amp to the box. Forget the other connector on the box.
Inside the box, the speakers will be connected together, when in series.
READ THIS COMPLETELY BEFORE DOING THE WORK...
To accomplish this, imagine drawing a continuous line from the + on the box, through the speakers, then out to the - on the box, just like the series diagram above.
Your jumpers are set correctly on the speakers, so don't touch them (the clear wires)...
Here's how it will go:
Choose a connector to work from.
Take the positive side of that connector and run a wire from the positive (+) post to the positive (+)side of one speaker.
Make a jumper wire to go from that positive (+) to the positive (+) on the other speaker.
Take the negative side of the same connector on the box and run a wire to the negative (-) side of one of the speakers.
Make another jumper wire and go from that negative (-) side of the speaker and run it to the negative (-) of the other speaker.
Viola! Series wired subs!
Before you fire it up, post up the pix of your handy work and send me a PM. The PM will go to my phone and I'll be able to check your handy work before you fire it up.
Right now, your speakers are wired in parallel. This means your amp is seeing a 1 ohm load and is overheating.
Rewire the subs
To get here, I referenced the online manual for the subs, here: http://support.alpine-usa.com/produc..._S06212011.pdf
Here's a pic of the install diagram for two Type R's and one amp (2 ohms):
Hope this helps,