Hi Paddy
Jacqui has explained most of it. The shadows will be black where as most of the moons are bright and are hard to distinguish across the face of Jupiter, except when they're near the limb.
However Ganymede and Callisto can be quite dark.
This is an image I did recently showing Callisto transitting and it's very dark! Yes, that's Callisto and not its shadow!
This is an image I did showing Ganymede transitting with Europa's shadow as well. While Ganymede is still very dark, you can see the difference compared to Europa's shadow.
The best way is to just know what you're looking at.
I use a program called
Jupiter 2 to know what transits are coming up that night, or to confirm what I saw last night, or to plan an imaging session next week for example.
Hope that helps!