To send your transport to a downed UFO you simply need to go in map mode and select the transport ufo interception button. I don't remember which one exactly but you should be able to do it easily. Simply don't forget that the smaller UFOs don't have an Alien crew so if you see your transport get there and return immediately then you don't need to worry: you'll still recover the downed craft and everything in it.
The problem with Apocalypse is that the game really only been balanced for real time. They worked on this aspect of the game in priority and then added turn based only to appease the fans. But if you really want to play Apocalypse to its full potential you don't have much of a choice than to go real time.
The game is still great... But I started to enjoy this game only after I began to take it as a game which is not related to X-com 1 and 2.
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