I am not sure what the best way to wire the sub woofers into my system. I have the following equipment:

Yamaha HTR-3063BL 5.1 Channel 500 Watt AV Receiver
Yamaha In-Wall 3-Way 120 watts Speakers
Yamaha NS-IW760 6.5" 2-Way In-Wall Speaker ( Center Channel)
2 x Pyle Home PDIWS12 12-Inch sub woofer 200W 8 Ohms, dual cone
Pyle Pro PTA1400 1400 Watt 2 channel bridgeable Amplifier

The speakers are pretty easy to figure out, what i am confused on is the subwoofers to the amp. Is it best to bride the 2 channels on the amp and connect the subs together then to the amp or to keep them on separate channels.
The amp says its rated to 325 W at 8 OHM So it looks powerful enough to run both subs either way. And will the Yamaha receiver give me problems controlling the bass since it only has one subwoofer post to connect to?

If anyone has some suggestions of the best way to hook up this gear let me know, since i Have to do the wiring before I put up the sheetrock in the basement I'm doing.

What I would do, is run aY-cable into both channels of the amp, then run one sub off each channel. You do want to make sure the gain control is turned way down, otherwise that amp can blow those subs. You shouldn't have any issues controlling the output from the Yamaha.

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.