So I have an Axe CPv3 and the 3 in 1 is fried. I have a great planes c-35 and a c-12 speed conrollers. Can I just use a y off the channel that the 3 in 1 went into and use the c-35 for the main rotor and the c-12 for the tail?

Sort of, yes. You need a gyro to run the tail motor. It goes between the receiver and the c-12. You will also need to remove the red wire on the servo connection going to the gyro. See this:
http://manuals.hobbico.com/hmx/hmxe04-gyro-manual.pdf

I do have a gyro I have been using. Sorry, I forgot to mention that in the original post.

So it is possible then?

what are the symptoms, how did you know it was the 3 in 1?

The main rotor and tail rotor didn't work. Upon taking it apart, I found the 3 in 1 had several transistors burned up.

Since I posted this thread, I have replaced the 3 in 1 with a great plains c-25 and c-12 with a gyro.

Its much better now and it all cost about the same as a new 3 in 1.