You need to apply the number of licenses matching how many access points will be terminated on the controller. If the first requires 32 and the second requires 64, that is how it should be distributed. If you purchased 96 licenses, they would arrive in a base-2 bundle, so you would split the licenses between both controllers, based on how many access points you have with each.
If the licenses do not come within the ballpark of what you need, you might have to contact the reseller you got them from or your local Aruba Sales team, so that they do.