I had come into the same problem when we transferred to QuickBooks online in September 2022. So after lots of research and looking online and talking with support, they said the same thing that you can only assign one workers comp code per employee. We have some employees in our shop who use 4-5 different codes depending on the type of work they are doing. This seems to be an issue I've seen people complain about for years. But QB has not tried to resolve it, just suggesting providing feedback to their software team.... Others have had to manually use spreadsheets to separate the time/wages to the correct code, which is very time consuming they complained.

I had to find a way to do this without spending hours separating the time between the 

We use QB Time.I made classes in QBO each class I made was all the codes we use in our shop.  This at least allowed our employees to separate their time by the right code. We still came into the issue of how we would then get the amount of payroll used per code, cause all these classes did was separate the hours by the codes. 

I did as you were asking @rachelleclif  I made a different Pay type for each comp code. And assigned these different pay rates to each employee.  Which seemed to work, but since I'm using QB Time for our timesheets I had to get it to work in QB Time as well. I used the Map Classes in the payroll item mapping tools which allows you to assign pay types to classes. You can get there by: (Under preferences in QB Time, then click payroll item mapping tools, Map overrides, Add Override, then click the class and what pay rates you want to assign per class). Make sure your employees have these pay rates assigned to them otherwise it will not work for them.

Once I did this, it all worked how I needed it to! I know your situation may not be exactly the same, but I figure this may be a good solution for anyone running into this problem who use both QBO & QB Time and have employees who use multiple workers comp codes.