Rewrite the whole paragraph and use a block to make it stand out more.

docs/config.rst

@@ -21,9 +21,16 @@ For full details refer to the `coverage config file`_ documentation.
 
 .. _`coverage config file`: https://coverage.readthedocs.io/en/latest/config.html
 
-**Important Note :** This plugin controls some options and setting the option in the config file will have no
-effect.  These include specifying source to be measured ("source" option) and all data file handling
-("data_file" and "parallel" options).
+.. note:: Important Note
+
+    This plugin overrides the ``data_file`` and ``parallel`` options of coverage. Unless you also run coverage without 
+    pytest-cov it's pointless to set those options in your ``.coveragerc``.
+
+    If you use the ``--cov=something`` option (with a value) then coverage's ``source`` option will also get overriden. 
+    If you have multiple sources it might be easier to set those in ``.coveragerc`` and always use ``--cov`` (wihout a value) 
+    instead of having a long command line with ``--cov=pkg1 --cov=pkg2 --cov=pkg3 ...``.
+
+    If you use the ``--cov-branch`` option then coverage's ``branch`` option will also get overriden.
 
 If you wish to always add pytest-cov with pytest, you can use ``addopts`` under ``pytest`` or ``tool:pytest`` section.
 For example: ::