First, I strongly recommend combining your samples for the annotation step. If you're including any kind of a de novo step, you cannot compare reads which were not clustered together, since there is no comparison between the OTUs or sOTUs. My suggestion (although I know others disagree) is that if you're using OTU-based clustering, you perform a reference-based step first, if this is an option. My preference toward reference-based clustering is that it allows consistency in annotation across studies: if you find OTU X and I find OTU X, then we're probably seeing similar sequences, which may mean we're seeing similar organisms.
The names need to appear in the mapping file. I suggest putting everything in the same mapping file so you can run the commands once. Demultiplexing is done independently, so combining the files has no effect. You can then use this mapping file with multiple_split_libraries.py