You might know this and if so disregard, you can use two scope channels and and the scope will subtract them and display them as if they were a pseudo channel. On some scopes, this is called the "math" channel, on old scopes it was a setting or was called invert and add. As long as you stay within range of your scope, you won't hurt anything.
The diff probe that I think you said you have? is a nice way to do this.
The difficulty with all this stuff is Common Mode rejection and the diff probe should be good in this respect. Ideally, you could take two big voltages and subtract them leaving just a tiny residual- like 14.00001 - 14 = .00001. What happens is the larger the numbers get, the poorer the subtraction goes. A fair CMMR spec might be 60 db or 1/1000. This is error in the subtraction based on how big the numbers are. At 60 db, this means if you had 10v, you would get errors of about 10v/1000 or about 10 mV- you couldn't resolve anything much less. Good CMMR requires precision matching of components so little errors don't creep in. Instrumentation amps are made especially to have high CMMR, the precision resistors required are all on chip and are trimmed at the factory- CMMR it can be over 100 dB, 10 PPM or 1/100000.
Good luck with your experiments. I don't quite understand what you're up to but at least this should give you some idea of what to expect.