Macinstaller does not depend on a hierachical source structure, it accepts all library files no matter where they sit. However, if the original source structure is very chaotic (including renamed files etc.) it might fail to silently find some referenced files and prompts you instead. The "default" name in the "New" field is always the name of the outermost folder you dragged on it - it assumes that models you want to install typically sit in a single folder with a useful name.