Superman, take out your deck, and it should say on the back. If not, are there RCA outputs on the back? If so how many? A picture would be best.
As for the speakers, you're sending them a clipped signal and they are distorting. Pretty much the deck is telling the speaker to increase the volume to a level where the power is not sufficient. So it clips in and out with the power. Also, after market stereos do more then double the power of stock stereos, and stock speakres are not made to keep up with the power, which is also why you will over throw them and bottom them out.
First thing is first, you cant amp stock speakers. You'll blow them.
If you have the cash, get a nice set of speakers. That will eliminate over powering them. So then you need to worry about under powering them - which is turning it up more then it can really do. For this you will need an amp. You can do temporary fixes with the deck, like turning down the bass (because that just eats power) and other such things, but in the end you'll be most happy with an amp.
Get a 4 channel amp, and you're going to want to set the front to high pass filter, and the rear we'll probably want to set to flat.
Let me know your budget and what you want, and I will help you out the entire way thru. I'm not on here very much, so PM me if you like and ill give you my cell number. When you wana figure things out you can give me a ring.