I'm doing true simulataneous sampling on the signals,JohnnyMalaria would you please give me a pesudo code? I do not get your Idea fully,Also I want to get the Phase info from the signals not the time delay between channles.
Please see that attached spreadsheet.
If your signal is steady over 100 cycles then this will work.
The calculations in the spreadsheet are very easy to do in MATLAB.
You can change the period and the phase to see how the calculation is affected. The calculated phase using the algorithm is shown. The key is to sample at a frequency that is not an exact multiple of your signal frequency. This is why the period is 99.9 in the example.
The example uses 3,000 samples. In practice, you could go much higher and increase the precision of the phase estimate.
Even with 3,000 samples, it is possible to get better than 1 degree precision for a signal sampled only 5 times per cycle

You should extend the number of rows significantly since this forum limits the size of the spreadsheet.
Note, this will only give phase results from 0 to 180 degrees (i.e., 270 = 90, 315 = 45 etc). If you need to discriminate then you have to employ the same algorithm but using a second reference signal that is 90 degrees out-of-phase with the first reference signal.