So I uploaded a plugin and all that. I go to turn it on in the ACP but when I go to set my perms to use the plugin I don't see it.
What do you mean by "set my per(mission)s to use the plugin"?
You don't set permissions for specific users or groups to be able to access or change settings on most plugins, as it's all done through the ACP more then likely (however their are some where this doesn't apply to).
Can you give the name of the plugin?
set permission for admin ?
admin/index.php?module=user-admin_permissions
maybe you want to set this permission n Board Messages will appear at config navigation.