Running Payroll (article)


PIMSY allows the system administrator the ability to run payroll for all users. This feature must be set up in the system and for each user. See articles Payroll System Setup and Payroll User Setup for details. Once payroll is configured, it is easy to “run” payroll when you have a schedule for your users to be paid (weekly, bi-weekly, monthly or other). This section on the menu is the exclusive area for running and managing payroll.

There is a small section for payroll on the invoicing page that tells the organization what to pay the provider. Payroll Advanced has its own screens and tracks all the different events and what needs to be paid to the provider, which events have already been paid to the provider, and has a review protocol built in as well.

Payroll in PIMSY is only for clinicians and salary employees.


Activity Paid Hourly or Flat Rate


Displays users who are paid hourly or by a flat rate.

Activity Paid by Percentage


Displays users who are paid by a percentage of their work performed.

QP Review / Team Notes


Any Team Notes in a Client’s chart will be recorded here.


History: history of all payroll or can be filtered

Do All: runs payroll for all users in the selected time period


Details: payroll information for the selected user – see right side of the screen




information on selected user

User Name

person to be paid

Payroll Num.

for user

Start Date

when you begin running this payroll

End Date

when this payroll ends

Final Total

amount the user will be paid


any additional text

Released by User


Released by User

populated from system

Released By Supervisor


Released By Supervisor

Populated from system

Payroll Paid

checked after this payroll has been completed

Use the Column Chooser if you need other columns in the window.


Go to Financial > Payroll Advanced and filter for the dates of this payroll.


Select the Do All tab or select a User Group. Click Yes. Add user group image

If you only have a few employees, click the View button to see the payroll lines individually in case you need to check them before running payroll.


Click Do All button to run the payroll for the selected dates. Once the payroll has finished, the Payroll Paid field in the right column needs to be checked one by one. Click the View button to verify the payroll for that user is correct. Insert image Checking this box locks the payroll just completed.


If needed, you can export this payroll and import it into your Quickbooks.


Use Case:

It is the first of the month and the PIMSY administrator at ABC Therapeutics needs to pay each clinician and salary employees for the first of two payments per month. The admin goes to Payroll Advanced and selects the time period for this payroll. The Do All tab is used to finish running the current payroll. The Admin Views each user to verify accuracy and to check the Payroll Paid box in the Details box on the right.

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