The main problem, in most cases, is that you don't know the pinout diagram of a flyback transformer. So, I shall try to give you a simple method to find the primary coil input pins and also the 0 V output pin of the HV secondary coil.
-=I do not take full credit for this=-
Step 1: How to Find the 0 V Pin Connection of the Secundary Coil?
With a common digital ohmeter it is impossible to find the secondary coil pinout because its resistance is much too high. The main HV output is simple to find : this is the big red cable with the suction cup, but you need to find the 0 V pin of the secondary coil on the flyback transformer. So, I give you a simple method to find this 0v pin :
a) You need a 24 V DC power supply and a digital voltmeter set in 20 V range. Connect the + input of your voltmeter to the THT ouput plug ( in the suction cup ) and the (-) to the 0V of your power supply. Then, with the +24V output from your power supply, test each pin of your flyback transformer. When you measure a voltage between 5 and 10 V you have found the 0 V pin of your secondary coil. This is very simple... Look at the diagram and the photo below :
Step 2: How to Find the Pins Location of the Primary Coil?
With a simple ohmeter this is very simple, you will find easily the primary inputs because the coil resistance is about 1 ohm
Step 3: How to Find the Polarity of the Primary Coil?
The purpose is to find the polarity of your primary coil. You need a simple 9 V battery. Connect a digital voltmeter set in 100 V range between the main THT output and the 0 V pin of the secondary that you have indentified in test #1. With the 9 V battery send a short pulse on the primary input, measure the spike of the voltage, then reverse the polarity of your 9 V battery. When you get the max voltage ( about a 30 V spike ) you have found the correct polarity of your primary coil. The (+) is the pin number 2 and the (-) is the pin number 1 in the main diagram.