Whatever triggered the test, the work in SmartCompaire is the same. You create a project, map source employee numbers to target employee numbers, map source pay codes to target pay codes, and load pay data from both sides as spreadsheet or CSV exports.
A comparison run then totals amounts per employee and mapped pay code on each side and records the difference. Rows found on only one side are kept as results, so a pay code missing from the target system shows up instead of disappearing.
Each difference is graded against the absolute threshold you set for its bucket and code type (how you group pay codes, such as Earnings and Gross), and labelled by your status rules. A row with no threshold for its bucket and code type is not graded, and a row without an employee or pay code mapping is labelled No employee mapping or No paycode mapping instead. Every run is kept in the project history, so you can fix a mapping, run again and compare the over-threshold count across runs.