Life on Mars said:
Get rid of wolves with bad/ok affinity. Get more wolves with good/excellent affinity. If you have certain wolves that have bad affinity but you want to keep them, you can buy and use Make Friends under Barter > Apples.
Overall, affinity isn't a huge deal as it only affects pack happiness, so I wouldn't worry about it too much.
Affinity does affect pack happiness, yes. But pack happiness can be a pretty big deal; pack happiness affects how quickly or slowly your wolves HP will regenerate. The lower your pack happiness is, the slower your wolves will regain HP.
If you don't plan on using explore or PvP much, then low affinity isn't something you'll need to worry about much, but if you plan on being somewhat active in explore, then it'll be a very good idea to make sure your wolves have good to excellent affinity so your wolves can heal more quickly when they loose HP
Going off on pack happiness, you'll also need to make sure all your wolves have different amounts of dominance. If you have wolves with the same dominance, your pack happiness will be affected negatively. This won't change anything related to your wolves affinity though.
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