No, CGI is good, and if I couldn't tell, then thats all the better.  I thought they may have used some physical models in some shots, and then maybe CGI in some others. 

Yeah, they've done a great job w/the CGI, IMNSHO.  The only times I've been able to tell it was CGI is when they've shown the cockpit of a Viper or Raptor fairly close up and you see the pilot w/o being able to tell who it is.  Most of the time, the pilot doesn't quite look "right". 

  But I am really gladd that they used some of the ships that were in the original show.  While I was watching the Mini-series, The first one that I saw that I remembered was the Long one with three Circles on it, and landing legs.  You probably know which it is by name, I have no clue.

That would be the Mineral Ship, sometimes called the Livery Ship.  It was the ship that is seen heading down to the surface of Carrilon in "Saga of a Star World - the BSG pilot - while Adama is speaking in to his log about sending mining ships down to the surface for the tylium they need.   

This site has a great primer on the more easily identifiable ships in the TOS RagTag Fugitive Fleet: Battlestar Galactica: Tech-Manual - Miscellaneous Ships.  All of the ships on that page have been recreated for TNS' RTF, plus a couple new designs and some of the more obscure older designs are there in the background - along w/bunches of other ships that appeared in a couple other shows.