I am going with a 1-wire alternator in my 69 camaro. I am going to run the alternator wire and the positive battery wire to the junction block. Is this the proper way to do it. I am using new Factory Fit wire harnesses. Also, I was told to unplug the voltage regulator and neatly tape of the regulator harness.

It would be better to use a 3 wire alternator. See reasons here
http://www.madelectrical.com/electricaltech/onewire-threewire.shtml
some 1 wire alternators can also be wired as a 3 wire. If you are going to use the 1 wire, wire it to the horn relay. it is the alternators job to power everything in the car and charge the battery, the horn relay is the mid way point between the battery and fuse box.