If you're using Book Designer, all you have to do is:
1. Click the "Make Sony Reader Book" button.
2. Go to the "Options" tab.
3. Add an external font using the area at the right side of the screen.
4. Define one of the "styles" to use that font.
5. Make sure that the appropriate parts of the document use that font.
For modern Greek, however, you really shouldn't need to do that. The standard fonts used by the Sony Reader have Greek letters in them. You only really need a separate font for ancient Greek because of the accents it uses - modern Greek doesn't have accents.