Multiple instances are the same as a single instance of your site, but linked together so you can quickly jump between them. This is ideal for companies that

• have multiple payroll systems/codes
• different rules for different depts (ie. union vs non-union)

In this setup, you can

• link employees between instances so they can work in both – read here (link to top article)
• single sign on, log into 1 site, jump to any of the others
• you can manage OT rules by each instance
• you can still run payroll from all instances from a single main instance (in the report there will be an instance selector)