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WebPT EMR Offboarding Guide

This guide is designed to help you navigate your WebPT EMR setup after onboarding and beyond. Now that you’ve successfully graduated from Onboarding, your Success Manager will be your main point of contact going forward.

Adding New Users - User Permission Management

For large organizations, it’s crucial to take a long-term view of permission management. This is true when adding new users or as user roles evolve. Check out this deep dive into the available permissions and what they mean to your organization. 

Managing Licenses

Depending on your contract, you may eventually run out of available therapist licenses. If this occurs, you can add more licenses using the Request License Adjustment option in the User Manager. Keep your Success Manager in the loop about any license additions to ensure your invoice is correct. 

Managing Your WebPT University Group(s)

When new users are added, we recommend adding them to their role-specific University group. This ensures they are automatically assigned to the correct training coursework. Click here for a refresher. 

Insurance Settings

As new insurances are added, it’s crucial to select the correct insurance settings. These requirements impact documentation requirements, modifiers, and billing codes, all of which have downstream implications for billing. Selecting the correct insurance type and related settings ensures that the patient documentation has the proper documentation and billing requirements enabled for the therapists. 

We’ve collected the most commonly used settings below. For a complete list, click here

8-Minute Rule or the Rule of 8s

One of the most common questions when adding a new insurance, is which unit calculation do I choose?

There are a few things to consider: 

  • Medicare always requires the 8-Minute Rule, and often so does Medicaid. 
  • Many commercial insurances accept the Rule of 8s. 
  • Generally, the Rule of 8s allows more units to be billed for the same duration of timed services. 
Rule Conflicts

In situations where the patient has primary and secondary insurances that follow conflicting rules, check your Payer Rules Company Setting to determine which units calculation the note will follow.

59 Modifier

If you need to add the 59 modifier manually to specific edit pairs outside of the Medicare requirements, you’ll need to use the Additional Modifiers workflow.

  1. Once the modifier has been added to the Company Settings page, you’ll need to enable it for each insurance.

  2. Then, the modifier will be available for use in documentation. 

Allow Therapist Assistants to Finalize Notes

This insurance setting overrides the related Clinic Setting, so it’s important to only apply this setting to insurances that specifically allow therapist assistant finalization or you may receive denials.

Require OMT Completion For All Patients

Selecting the Require completion of a WebPT Outcomes OMT insurance setting will require every evaluative note (Initial Evaluation, Progress Note/ReCert, Discharge Summary) to contain a full, completed OMT survey (each answer input, not just the score) prior to finalization for all patients with this insurance. This setting is only recommended for Members reporting the MIPS HM Measures or for Members actively managing their WebPT Outcomes.

Save Updates

To save any changes you’ve made to existing insurance, click the Edit Insurance button.

Adding New Locations - Clinic and Company Settings

When adding new locations, ensuring the Clinic and Company Settings match your existing setup will reduce the risk of inconsistent EMR workflows and downstream billing implications.

Clinic Settings

Allowing Therapist Assistants to Finalize Notes

Enable the Assistant Note Finalization clinic settings to allow the action and make your selection for any verbiage that you’d like to include on the note. You’ll also need to ensure the assistant has the appropriate user permission as well.

Medicare Fee Schedule

Your Medicare Fee Schedule settings do not automatically default to the clinic’s region. Please choose the closest identifying region. This region is used as a guide for how close a patient is to the cap, not an exact calculation. Select Non-Institutional (common) or Institutional (UB-04/Hospitals but not if using RevFlow/WebPT Billing). Your clinic will receive an alert at each log-in until the Regional Location is selected.

Place of Service

If you are providing service outside of the clinic location, select the Yes radio button for this setting. This allows users to choose the correct place of service on the patient case and patient note level.

WebPT Outcomes

If you’ve purchased WebPT Outcomes, follow the same settings you’ve chosen for your other locations. These settings force specific behaviors and include satisfaction questions for patient perception calculations.


When enabled, you’ll need to include a referral for every new patient. This may not be desirable if you treat a lot of self-pay or direct access patients. These settings do provide better reporting on referrals and referral conversion metrics in Analytics reporting.

Company Settings

Additional Modifiers

If your organization needs to use specific modifiers, these can be added to your company settings. Modifiers must also be enabled on the insurance level before they can be included in the note.

Initial Exam Case Copy - allows you to make cases a little easier. 

Enable this setting to easily copy the patient’s most recently finalized evaluative note into the patient’s new case. This functionality is valuable in situations where the patient insurance changes in the middle of their treatment.

Analytics Reporting

In the future, WebPT will sunset the clinic-specific EMR reports and drive all reporting through the Analytics tool. Many front-end users and therapists who rely on productivity and missed note reporting will need to transition to Analytics. 

WebPT University Training

  • Analytics 101: This program is designed to help users get logged into Analytics and understand how to approach the most commonly used reports, all in 45 minutes or less! Enroll here.
  • Analytics Certification: Designed for users who need to understand the nuances of their data in Analytics, this 3-hour course and 60-question exam can be completed here

Top 5 Analytics Reports

These are the Top 5 most commonly used EMR reports across our Members. Each report explores three to five specific reporting scenarios.

  1. Billed Units: Your go-to report for answering questions about documented billable visits, locating billed CPT Codes, understanding the Place of Service mix, and audit your therapists’ billing practices. 
  2. Patient Notes: View patient details for all finalized billable notes, including treating diagnosis. 
  3. Scheduled Visits: Manage your scheduling practices by providing a complete view of past and future appointments.
  4. Patient Case Status: Dig into information about the patient’s case including primary insurance, referring physician, and total visit count. Monitor patient progress by reviewing last and next appointment info.
  5. Referrals: Identify physician and marketing referral sources and gain insight into referral conversions, the average time to conversion, and common referral diagnosis codes.

User Management

There are three main Analytics User Roles that dictate default report access. Use the Bulk User Role Management page to re-assign user roles.  

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