Must changes to bitcoin.conf only be made using the GUI settings options?
Or can I edit the file with a text editor such as Notepad?
I believe you can edit the config file with a plain-text editor. However using the GUI is less likely to cause the file to contain invalid data that will cause alarming or potentially impoverishing problems.
If there are reasons to not use the GUI to change the configuration, using the command line options may be safer than editing the config file.