Plugin basic permissions needed for players are all given by default.
All the command permissions use the following format: skills.command.[groups...].<name>
Where <name> is the main command name (not their aliases) and [groups...] are the group's main command names.

Command	Permission
/skill show	skills.command.show
/skill select	skills.command.select
/skill change	skills.command.select
/skill user souls	skills.command.user.souls
/skill user improve	skills.command.user.improve

Note that some names are not command groups, they're command arguments.

If your permission plugin supports wildcards * you can use that as well. For example skills.command.user.*
An ideal permission plugin suitable for any server is LuckPerms.

To take away the default permissions given to players, you have to give them a negative permission. Different permission plugins have different ways of doing this. It's always recommended to use the plugin's commands to do these.
For example, to take skills.command.select permission using LuckPerms, you need to do /lp group <group> permission unset skills.command.select

Permission	Description