I got the large 32mm nut loose and everything. I got the cv to pull out of the rotor. Howeveer, I can't get the balljoint to seperate. It says I need a ball joint sperator. I thought there was another way to do all of this. Can someone PLEASE help me? The car is all apart as I type!

Don't fool with the ball joints, unbolt the 2 lower strut bolts. Make sure you take the clip holding the brake line to the strut, and move the knuck out and back. The axle will come right out.

Now, will I be able to get the new axle in the same way without damaging it?

Yes. I've R&R'd axles using that same method, and none were broken.