Can I upload my linked drawings (xrefs) as separate files?

Yes. Put them in the same project as the drawing that links to them, as loose files, a zip such as an eTransmit package, or a whole folder. AutoMEP matches them by file name and ignores capital letters, spaces, underscores and hyphens. If a file was renamed, for example S-GRID-v2.dwg for a link to S-GRID.dwg, AutoMEP asks once whether it's the right one. One linked file serves every drawing in the project that uses it. If you upload a newer copy with the same name, the newest one is used from then on, and the older copy is marked in the Files list. AutoMEP only reads your linked drawings: it edits the drawing you asked about, never the files it links to. You don't need to bind anything first.