Balancing manuals and management of people

I’ve starting using SCS tools in my job as it applies to management of people. When looking at my personal life, I can more clearly identify when I am trying to use a manual for people, but for some reason I am finding some confusion around applying it at work. For example, I have a team member that shows up late without notice, against department policy that says we should notify our manager within an hour of tardiness. When this team member pushes the limits on what the guidelines are, she sends emails with “condescending tone”. For me, I want to just address where she is not meeting expectations (as it applies to department guidelines). On the flip side, my boss and the office have an expectation of how you treat people with respect in addition to respecting her manager’s authority so I need to address the tone of her emails and how she interacts with team members. How can I work on balancing this role in management with situations where the culture calls for somewhat a manual for how people behave.

Hope this makes sense. I’ve considered getting a coaching call on it. Thanks!