Eva - We have worked with clients that do this and would recommend a very similar set of things in this that we would for a multiple marketing automation to 1 SFDC (even if it's all Eloqua) or multiple SFDC to 1 marketing automation. The crucial thing is really about establishing the governance and business process of data priority, etc. then making the technology bend appropriately. I'd point you towards the articles in this search http://topliners.eloqua.com/search.jspa?q=integrating+multiple+instance
Best,
Lauren