Sahs,
Although the options are somewhat limited, the fax cover sheet can be readily customized.
In Updox, go to Admin...Fax settings...Cover sheet.
You might begin by erasing the "default" heading (for us, that was the blocky "Medical Fax" that is right-justified.
Type the text you want, select it, and use "Heading 3" for "Font format". You can use the space bar to move the header, and you can also play with the other heading font formats. You can change font size, etc.
You can also copy an image from elsewhere (e.g. your practice logo) and paste it into the coversheet.