OK found it:
For the SELECT switch, you need to determine the output of your head unit. My guess is the 1-8 volt but merely a shot in the dark.
LP FILTER is at what point you want it to stop allowing the frequency through. The lower the #, the lower the tone it will block at. My advice is start at the highest setting and play with it from there to what your personal taste is..can't damage the amp with that.
SUBSONIC FILTER, I'd go with none or 15HZ. Alpine recommends the 15 when using subs such as 10" bass speakers if the sound seems less distorted versus the none setting. 30HZ is for ordinary speakers (such as a mid bass).
I'm taking a stab you don't have the instruction sheet with this amp. I found it at the link below, only 2 pages so it will download fast..this is where I got the information I listed on this post. I saved a copy in my email, you can either PM me your email and I'll send it or search for Alpine PDX-1.1000 manual at this link:
Sorry for the delayed response. Here in MA we've gotten over a foot of snow so I've been dropping in between snowblower runs
I'd see how you like the sound of it and go from there as to your ultimate solution. You may be satisfied as is with the 2 subs. If so, you've got a spare sub in case one pops or can sell one. If not, sell or trade your amp for another. Just make damn sure if you go that route that the new amp is 1Ohm stable. If it is, use the diagram for the 3 subs you posted and you'll be golden.
Keep me posted how it sounds once you mess with the other 3 settings..