This question comes up quite frequently.
The feature you want is not supported directly by FontCreator. You can create the extra glyph easily enough, like creating æ from a + e, but to get Windows applications to substitute that when you type a, then e, or ã then o in your case, requires two things:
- The application must support OpenType Features
- The font must contain them.
See this tutorial on Adding OpenType Features for a relatively easy way to add them. You can also use VOLT, which I found too difficult.
Not many applications support OpenType features. Word 2010 will do, but currently InDesign is one of the few choices. This is why there is currently little incentive to add OpenType feature support to FontCreator, although it has been requested several times.
To the same thing in applications that don’t support OpenType, you could use Autocorrect, or define shortcut keys, or use a custom Windows keyboard.