What are the differences between Small World and SW Underground?
There's a great "first look" at Small World Underground here.  This section in particular caught my eye:


  
  After you choose a map, do not use powers that depend on features
  that are not present.
  The following features are considered equivalent concerning their
  interaction with powers:
  -- Black Mountains / Mountains
  -- Mudpools / Marshes
  -- Mushroom Forests / Forests
  -- Mines / Mine symbols
  -- Mystic Crystals / Magic Symbols
  -- Rivers / Seas &amp; Lake
  
  
  I would add that some of the special powers in SWU duplicate racial
  powers in SW, or vice versa. If they happened to get combined
  (Immortal Elves, for example), I would simply put them back in the bag
  and draw again. [Edit: Many such combos are OK, since they enhance
  each other -- e.g. Commando Ogres, Vampire Sorcerers -- just like
  Pillaging Orcs in SW.]


From the sound of it, there has been some effort to "integrate" the two different games so that they are not basically incompatible (i.e. making sure there are analogous terrain types), but this only goes so far.  Some races may not work, and some races may get special powers that duplicate their racial powers.  So it could prove a bit annoying making them work together, if you like things to be really neat and tidy...