Modifying default report forms

My company operates 4 different Sage 100 Contractor companies, with different tax ids and and banks and logos and entity names.  I'd like to customize the default system report and landscape report forms to get our branding on them, reduce our color print count, and maximize the data grid area on the form.  Obviously I can create the form, I can name it System.Report, but when I save it as a company form, I seem to still be getting the shared form that is is in the \Sage100Contractor\Report Forms directory.  Can I just remove that file after creating a System.Report in every \Company\Report Forms directory?  Will it get put back there after every update? Will it break anything? Is there a "right" way to do this that I am missing?