Well, in Blender you can choose which card(s) you use as your compute device(s), and you can use a separate card for that, or even multiple cards without SLI (Blender works best with multi-GPU without SLI).
I don't know much about the Autodesk programs, but from what I heard, they only use GPU for the viewport and for simulations. And I guess the viewport is always rendered by the GPU your monitor(s) is(are) plugged into, so for that your extra gpu would not make a difference (unless you use SLI, though you'r planning on getting different GPUs). Maybe Maya/3DS Max allow you to choose which GPU(s) you want to use for simulations, but I don't know if you do that kind of thing.
You didn't say which render engines you'r using with your Autodesk apps, but most popular engines used don't use GPU, so your extra card would not help there either. If your primary focus is Blender Cycles rendering, go for the extra card, it will help a lot! But otherwise the extra card might not even be used.
What are the renderers you use most? Because, if your primary renderers don't use GPU, then the extra card will not even make a difference.