Can I use WF to take the values from a custom record and change them on an employee record? I see the Goto Record action but what I want is to change some field values once there.

You'd have to use a workflow action script

Is there a name for this WF action script? Set Field Value?

No, it's a custom script that utilizes workflow setup to initiate

Is there any relationship between the records? Maybe you could put the value onto the Employee with a summary saved search field. Then use a WF to copy to a Stored field. Might be easier to do it as a simple afterSubmit script on that Custom Record as Kevin suggests.

if you put a join to the record that holds the values you can easily access them via workflow / setfieldaction "from" record | field