Quiet 6x9s and Sub tuning

Hi, I'm new to this forums looking for a little help.

Right now I am running an eclipse head unit and a 12" memphis m3 to a memphis power ref. 1000 mono block amp. The first question I have is how can I properly tune the amp to the subwoofer without being afraid of ruining the sub. I believe I have the gain set right. But I`m now sure where to place the crossover freq and I have no idea what a subsonic setting is. I'm slowly raising the bass boost, but not sure how much is too much.

The second question I have. I recently purchased a pair of RF power 6x9s. I was told that the head unit would have enough power to atleast power them. But after hooking them up, they don't get loud in any way. It sounds as if they don't go past 10. I have them wired into the stock speaker adapter and then plugged into the car. If I do need an amp, would I need to rerun the front speaker wires to the headunit or the amp?

how can I properly tune the amp to the subwoofer without being afraid of ruining the sub.

That part is taken care of in the selection of sub vs. amplifier power.  The criteria is RMS output of the amp vs. continuous power handling capacity of the sub.

I believe I have the gain set right.

If you preface this with "I believe...", then you probably don't.  Did you use proper test tones?  See my response in this thread for a list of threads to read for the proper procedure.

where to place the crossover freq

Try 80 Hz low pass for the sub, and a corresponding 80 Hz high pass for the mains.  Use the test tones here, too.

what a subsonic setting is

If your box is vented, use this to correspond to the tuning frequency of the box, or just slightly below it.  If the box is sealed, leave this off, or at flat or minimum, as it will not be required.

I'm slowly raising the bass boost, but not sure how much is too much.

IMO, a little bit is too much.  Think of a bass boost as a type of band boost...it provides a higher power level to a narrow band of frequencies.  In every case, it corrupts the overall frequency response of the sub.  Especially consider this:  boost freqs are in the range of the natural boost that will be (or currently is) attained with the sub installed in a vehicle.  The natural boost I'm referring to is called "cabin gain".  The rise in freq response due to cabin gain is right in line with the inflated boost built into the amp (just a +3 db boost sends twice the power to that band), so you end up with a much higher peak in those freqs than you bargained for.  Don't use it just because it's there.  With a more critically tuned ear, you will immediately notice the loss of sound quality when you use the boost.

For your 6 X 9's (are these rear speakers?), I suggest you have determined that the head unit isn't powering them to the level you want so you should go ahead and install a two channel amp to power them.  Speaker wiring will be from amp to speakers.  Tape off the OEM wiring connectors so they don't touch to chassis.  The Eclipse head unit will function purely as a preamp, and RCA connectors will provide the signal to the amplifier.

If these are rear speakers, and I hope so, what do you have for the fronts and how are they powered?

Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.

The 6x9s are in the front, the stock speakers are 6x9 all the way around.