Hi vlsi
You can easily use VeloceWired for multi-die or even for stacked-die applications. You just have to import the two dies (you need the die outline and the pad positions) and the package artwork and start drawing the bondwires.
Any bondwire between the dies and the package or between the two dies can be drawn by a simple two click procedure. Downnbonding wires can also be designed using the same methodology.