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NMM was made with Skyrim in mind. It has yet to give me an issue with Fallout 3 or New Vegas. NMM isn't compatible with OBMM (mainly because that was just a ****ty program), don't even try it with Morrowind, I recommend manual installs for that on, unless the mod comes with an installer, like Morrowind Overhaul.
From: zotobom | #004 Roniello,they can both switch. I would choose NMM just for that "download to manager" button on the Nexus I think this is bugged or something as it downloads are compatibility patches and not the actual mod. .