By "the software" do you mean TMG?? TMG will generate whatever options you ask it to produce in regard to indices, table of contents, headers and footers, titles, etc. The book will be created in the word processing software of your choice. As to if your wp software accepts the options you choose in TMG is another matter which TMG cannot control (I would have no idea why they won't accept your choices). Cites will print out in either footnotes or endnotes. BTW, TMG will give you a 30 day trial use of the entire program before you have to pay for it.