@Lorinda --- I am not involved with the development of this plugin, but it looks like you are trying to use multiplexed sequences where demultiplexed sequences are expected.
Use demux emp-paired to demux, then provide that is input to itsexpress.
Again, I am not involved with the development of this plugin, but I would suggest that maybe that kind of functionality doesn't make sense in the context of this plugin. I think the general design idea here in QIIME 2 is to compose modular building blocks of functionality. Each plugin/method should do one thing, and one thing well.