That part of it is currently working correctly.
I've had some issues with permissions, sometimes they act a bit odd, but if you try the opposite approach, then it works (for example, if you're having trouble allowing one react to a single group and it's not working, try setting it to be DISallowed by all OTHER groups). But after some minor testing, you should have the permissions system figured out.
Also careful if you're doing site updates or IPS Support is checking out a problem: if Advanced Reactions is disabled, suddenly EVERYONE has full access to ALL reactions, even if they're some +100 rep reacts that are rarely used and only by admin. To fix this, I temporarily disable the reactions that I don't want anyone to use when site maintenance is being done.
Now I'm just waiting for @MIXOH to add the ability to have individual max reacts/day for each reaction and group, that would make a big impact on our site and how it is used.