Company sites (or sites) are simply various physical locations in which you operate your business.
This could be as simple as your office name, client site names for employees who work away from your normal workplace right through to multiple different sites in different countries. This field is a filter option in reports so you could show a list of time off for all employees in Site A, for example.
Specific departments, currencies and even time zones can be set to a site. You can also assign specific branding settings to a site also in site template. To set up a new branding type, browse to:
Administration > Company > Settings > Branding Settings > Add
Site level timeoff settings allow you to have different time off rules on a site by site basis. For example, the holiday year starts on January 1st in UK but starts on April 1st in US. These site level timeoff settings will override the main time off settings which apply to those employees whom are not attached to a site with site level timeoff settings. Click here for more information on Site-Level Timeoff Settings.
To add or edit sites, simply to go:
Administration > HR > Data Management > Sites
If you are still unsure, leave site level time off settings unchecked for the time being.