The best way to wire up a system like that before the drywall goes up is to put in separate wires for each thing. That way, if you interconnect the two or not, or change it five years from now, you don't have to rip up the wall to do it. We generically call this "doing home runs." Each speaker's wire is run to "home."

Then you can deal with the signal situation later.

I think you're saying that the Yamaha has one line level ( = RCA jack) subwoofer out, and the Pyle amp supplies audio to the subs. anyhomeneeds has the right answer there.

Don't even think of running the power amp in bridged mode. The subs are 8 ohm, so two in parallel are a four ohm load. When an amp is in bridged mode, it usually wants at least and8 ohm load. One way to look at this is to think of the bridged amp as two amps in series; each amp is capable of a four ohm load, and since the amps are in series, they need to see the equivalent of two four ohm loads in series, which is eight ohms.

If the amp is made to output to 2 ohms, then you could bridge the amp and put the speakers in parallel. There's no point in bridging the amp and putting the speakers in series because bridging increases the power but the higher impedance speaker load decreases the power that the amp can put out. Besides, as anyhomeneeds points out, you'll probably have the volume way down on the power amp, thus not need anywhere near all of its power.

The answer to the next question is that, before you run Yamaha's auto level and EQ program, set the volume of the subwoofer amp so that things sound right to you, then let the Yamaha correct it.