I would like to run two or three different wikibase instances with WDQS, to achieve this will I need multiple services or can I achieve this through using only one service?
Topic on Talk:Wikidata Query Service/Implementation/Standalone
Right now the easiest way to do this would be to setup multiple services.
Technically blazegraph can store multiple wikis withing a single instance, as it has a concept of separated namespaces, I'm not sure if the WDQS updater supports selecting which namespaces updates go to out of the box though!
If the updater does / did have a namespace option, you would be able to run an updater for each wiki with a different namespace all pointing to the same host.