they include it with the program, but it is prone to making the game unstable. It would be a far better Idea to go out and get Orion Pirates and play that in an earlier era if you dont want to deal with the X-tech.
But, if still want to give it a try, do the following:
Back-up or delete all your saved games
Go to ...\Starfleet Command II\Assets\Scripts\Campaigns\ConquestBonus
run the PlayBonus.bat (This will replace all the meta campaign files with Conquest Campagins)
Run SFCII and pray that it works...
If SFCII refuses to run in Campaign mode afterwards, you will have to go to the same folder and run the PlayNormal.bat to return the campaigns to normal. If it refuses to run after that, you will have to reinstall.