@Nonlin
Personally, as long as it’s getting you’re intended job done, I think either way is going to work. I think the biggest issue is going to be the size, because I would assume that two individual “objects” would be a bit bulkier than a single object with two emitters.
My best advice is to go with what works for you, but I don’t think you should have any trouble with two emitters on a single system.
I hope this can help!
-Zen