OK, so you're talking about "p implant" or "n implant" (sometimes called pplus or nplus). Fair enough - you have a layer to define the implant that's used on the diffusion opening (or active area).
You typically have a layer to define nwell (or pwell, depending on the type of substrate). I don't see why you'd need two layers to describe that? So I still don't really understand your question. If your transistor is used on a p-substrate, there's no need to draw a well around an nmos transistor (but there would be around a pmos transistor).
Note that this is nothing to do with Virtuoso at all - it's to do with how the technology has been set up and what mask layers you actually need for manufacture.