Use of both 'query' and 'enquiring' are valid, but have different connotations and respective syntax.
1. Employees are 'querying' their overtime payments.
Here, the employees know about their overtime payments but think the payments may be wrong (or know that they are wrong, so they're questioning their accuracy).
2. Employees are enquiring [no 'e', I don't think there's a single gerund form ending 'eing'] about their overtime payments.
And here, they're asking for information about said overtime payments.
There's also the 'inquiring' variant as mentioned by Josh, but this spelling is usually used for more formal/high-powered situations (like a government inquiry or legal inquiry or relating to investigations etc. or so it is in British English, I'm not sure about American English).