To say this first: I really don't like that Thermo Stripping Buffer. It never satisfactorily removed all the antibodies, as verified with ECL, no matter which recommended protocol I tried. As GNANA pointed out, to be really sure, you could verify removal of primaries by incubation with only secondaries and then ECL.
The hands-down best stripping buffer protocol/recipe I have ever used is incubation in 100 mM NaOH, 2 % SDS and 0.5 % DTT for 1 h at 55 °C. Sounds kinda harsh but it actually works several times on the same PVDF membrane. Have not tried with NC.
As for identification of the bands I can recommend a little trick, in case you are detecting digitally. After you have detected your chemiluminescent signal, you take a regular photo of your membrane at the exact same position. If you overlay those two images in a capable software (like Photoshop) you will have the exact location of your signal on the membrane. And if you do this with the same membrane but different antibodies, you may exactly overlay those two overlays by the dimensions/outlines of your membrane, and see the location of both signals. Hope that's not too confusing.