Text that I don't want to change, changes when I apply a font scheme
You have selected Font Scheme options that dictate the changing of all text. To maintain manual formatting, you need to turn off these options.
Not all my fonts are formatted when I use a font scheme
You have text that was formatted manually. You can ensure this text is also formatted by a font scheme.
My text changes size when I use a font scheme
Text size is one of the characteristics that is stored in a font scheme. (To ensure that text is not affected by a font scheme, next time, format it manually before you apply the font scheme.) To return your text to the desired size after you've applied a font scheme, you'll need to reformat the font.