[Jellby]

Then I guess it's the same as with any other font, at most you'd have to specify the font-variant in the @font-face. You need to define the font in the CSS:

@font-face{
  font-family: "My smallcaps font";
  font-variant: small-caps;
  src: url("../relative/path/to/the/font.ttf") format("truetype");
}

body {
  font-family: "My smallcaps font";
}

Then you have to include the font.ttf file in the epub and add the corresponding line to the <manifest>.