Hi! Glad to hear you made it!
The HADDOCK score is not a proxy for binding affinity, but better scores could be indicative of a preference of binding (see also Compare HADDOCK scores - #2 by amjjbonvin)
The rule of thumb here is that the more the system remains constant the more sense it makes to compare the HADDOCK scores. What we typically suggest in this case is to take an example in which you know the answer (e.g. two molecules with different minor units in which you know the binding preference in your case) and test if you can tell the difference from the scores.
PS: remember that this forum is searchable, lots of discussions about comparing scores can be found 
Cheers,
Marco