what is difference between people and groups and permissions in site settings?
i created some custom groups from _layouts/15/groups.aspx page and these not showing in /_layouts/15/user.aspx page.
"People and groups" page shows all groups and groups members, "Site permissions" from the other side shows you only those users and groups, which has permissions assigned on this particular site.
Since you created a group, but didn't assign any permissions yet, the group will not be under "Site permissions"
People and groups:Specify users and user group who have access to this site and any sub site which inherits permission
Site permissions: Define capability of each user and or user group can perform on this site and sub site inheriting from