Our company just started back to work last week after the government shut down. We have been paying our employees their normal wages with our PPP loan but now with them working in the field we are paying an additional hazard pay of $3/hour extra. I do not know how to set that up correctly

I'm glad your business was up and running since last week, @kv4. I'll guide you through setting up the additional hazard pay for your employees in QuickBooks Online (QBO). 

You're on the right track in paying your employees using the PPP loan. Since you're now paying them an additional hazard pay of $3/hour, I'd suggest creating a pay type for this. This way, you'll be able to run their payroll with this amount. Before that, you'll have to consult with your accountant to confirm the specific pay type you'll need to use. Once verified, proceed with the steps below. 

1. Go to Workers from the left menu. 
2. Select Employees.
3. Choose the employee's name. 
4. Click the Edit (Pencil) icon beside Pay. 
5. Go to the How much do you pay [employee's name] section. 
6. Choose the pay type that fits the hazard pay. 
7. Hit Done. 

For the detailed instructions, check out this article: Add Or Change Pay Types. 

Once done, you can now create paychecks for your employees. I've attached a screenshot below on how the Hazard Pay looks like in the program.

Also, you can enter an expense, check, or bill to track what you spend on other eligible operating expenses. Please make sure you're properly categorizing them. After that, I recommend running and customizing the Profit and Loss report. From there, you'll be able to view how much you're spending with your PPP funds. For more details, see Step 2 - 3 through this article: Track How You Use Your Paycheck Protection Program Loan. 

I'm just a comment away if you need further assistance. Wishing you and your business continued success while using QBO, @kv4.