Do not add the numbers yourself. The software will correct the sequence of numbers when you insert or remove notes. Do not write the notes as end-notes at the end of the text. Do not add indents of any sort to footnotes. Many people add complex indents and tab marks to footnotes in an attempt to make it look neater, but this makes editing the footnotes much more complicated.
Modern printers can produce italics and so there is now usually no reason to use underlining.
If you think italics are not clear on the printer you are using, you can use underlining, but italics is normal. Do not use bold for book titles. Do not use underlining and italics together, i.e. do not write Title of Book . You can use either single or double paragraph breaks, but be consistent. This can be done by setting an indent using the Ruler.