If you are indeed talking about installing XCI files: Yes. As long as you are inside emuMMC/emuNAND and have set up your folder as "emutendo", then anything that you install will go into that folder.
There's no difference between installing XCI or NSP files, at least if you look at the outcome. Those installers that are able to install XCIs are just converting them to NSPs before.
However, if you're talking about mounting XCIs so they are getting an icon on your homescreen, then no: They are technically inside your nand. If you're inside your emuMMC/emuNAND, that nand is most likely the hidden partition on your SD card.
However, I guess the main intention of asking this was to make sure that whatever you do inside emuMMC/emuNAND does not interfere with your sysNAND which uses the Nintendo folder instead. Don't be afraid, that does not happen.