Regeneration specifics: activation of the ability in combat
In the declare blockers step, the attacker must specify the order of the blocking creatures.  

What that means, in the scope of your question, is that the owner of the 5/5 creature must declare which of your 4/4s he is going to deal damage to first.  As such, you have a pretty good idea which creature you want to regenerate: the one the attacker put first into the firing line!  Unless something else happens, that creature will take 4 damage and be regenerated, the other creature will take 1 damage, and both your blockers will survive.