The amp gauge is not working and with the cluster out I checked the voltage on the red and the yellow leads and get a 12 volt reading off of both seperatly Is this correct?
Yes, that's correct. The '66 Amp gauge is simply a voltmeter connected in series to measure voltage drop. If the alternator is charging and the current is flowing INTO the battery the needle swings to the C side. If the alternator is not keeping up with the load and the current is flowing OUT from the battery the needle swings to the D side. Most '66 Ammeters crapped out a couple years after the cars were delivered. There are internet articles on converting it to a voltmeter, or you can replace it with a new reproduction or an aftermarket gauge.
Yes if you are measuring the voltage (wires disconnected from gauge) (engine not running) individually you will get 12v reading on both. Your gauge reads both those voltages and the differance between them when the engine is running