It looks it is impossibly to save few separate XML documents into Windchill by the only Save to Server or Check In. For example, if you have few DITA topics, but you have no map file, you should save separate documents into Windchill one by one. The same, if you have S1000D XML Data Modules you should open and save them to Windchill Server one by one.
Usually WGM technology proposes to upload all source files from local disk to Windchill. But Arbortext cannot do it. The only possibility for Arbortext - to save root document with links to chield documents.
I believe such functionality like "import many XML files into Windchill" should be realized in Arbortext.