You still create a map in a BizTalk project in Visual studio. Select source and destination schemas, but instead of mapping using the visual tool (links and functoids) you click on the mapping canvas and under properties choose "Custom XSLT path" and choose
your xslt file. Now the map will use only this file and ignore any visual mapping. Deploy the project and use the map as you would if it was a "normal" BizTalk map.
Note: If you change your xslt after you have deployed your project, changes doesn't always apply until you either restart Visual Studio or clean the project (I believe it is because the .cs files still holds the old xslt)
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