What to do when all basestars are in the Cylon Fleet board?
The rules for placing ships on the Cylon fleet board are awkwardly placed over two pages and it appears you missed the second section.  The situation is considerably more dire for the humans that how you played it.  The basestar shows up on the main game board and usually brings a party with it.


  If all ships of the appropriate type are already on either the
  main game board or the Cylon Fleet game board, the current
  player finds the highest-numbered Cylon space area on the
  Cylon Fleet game board that contains at least one of that type
  of ship. He then moves all the ships in that Cylon space area
  to the corresponding space area on the main game board.