I am interested to know what to do without the master reference
do you by any chance have an example of how this calculation works? (or how it is done?)
I don't have an example.
You need three time interval counters that are connected to a computer to collect the data. Depending on the counter, the connection can be via GPIB, serial, ethernet, or whatever allows you to gather the data. As mentioned earlier, you measure A-B, B-C, and C-A. In each case, you're measuring the time delay between the rising edge of the signal on Channel 1 and the rising edge of the signal on Channel 2. Depending on how good your three oscillators are, you might be able to just connect them directly to the counters. For high performance oscillators, it might be necessary to provide various complexities of pre-processing of the input signals to enhance the small differences and bring them out of the noise. Converting a sine wave input to a square wave is a likely first step. Ultimately, you'd have to go to a DMTD system configured for 3-cornered hat operation.
You'll probably need to write a program that queries the counters and logs the data.
Once you've got the data, you import it into Stable32 or Timelab to do the analysis. They're both freeware. They process the data and produce nice graphs that show you the performance of each oscillator.
Of course, there are many details that have to be considered to get usable results. This isn't a simple or plug-and-play operation.