Yes.
You have to be sure that the new ship set is in a file in your Pictures/Race/ folder "named" for the name of the race as it is spelled by its files. (EXAMPLE: I named the Cardassian ship set Card_ That means that the Cardassian Folder in the Pictures/Race folder MUST be named "Card".)
The same goes for any race you download if it does not create its own folder, you'll have to do it your self, and its quite easy to do.
Once the new race is in its own folder (PICTURES/RACE/NEW RACE) just start a game, and select "Add New Empire" in the Players set up window. Just go through the races until you find your new race, and then set them up. Start a game, and go to the OPTIONS icon, and select SAVE EMPIRE, and save the empire you've made by what ever name you choose. I always save mine like this: New Race 2000, New Race 5000 as an example for doing it this way makes it easier to know which race has which Racial points.
Hope this answers your question.
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"We've made too many compromises already, too many retreats! They invade our space and we fall back -- they assimilate entire worlds and we fall back! Not again! The line must be drawn here -- this far, no further! And I will make them pay for what they've done!" -- Captain Picard STNG
New Age Ship Yards