This should work:
| morph1 morph2 |
morph1 := Morph new.
morph1 color: Color red.
morph1 extent: 200@200.
morph2 := Morph new.
morph2 color: Color green.
morph2 extent: 50@50.
morph1 addMorph: morph2.
morph2 position: 100@100.
morph1 openInWorld.
Result:

Note that the positions are absolute, if you want relative positions, you should do something like:
morph2 position: (morph1 position + (100@100))
If you add Morphs to the window, you can take a look at SystemWindow #addMorph: fullFrame: which offers the best options for positioning subfiles. Morph also implements #addMorph: fullFrame: but for some reason this doesn't work for me in Pharo 2.0.
: Pharo CollActive book
" " 2.