Simply put, yes you can.
If you have not built the ship yet, you can simply EDIT The design and add the engines.
If you have built the ship, you can redesign it, with the engines, rename it "your design name" and "A" for example. Then simply retorfit the ship you built.
Go back to the design screen, and make the old design obsolete. I have "Hide Obsolete" selected in my game, so when I make something obsolete, its gone from my design window.
Hope this helps.
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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!" -- Patric Stewart as Captain Picard
UCP/TCO Ship Yards