You would definitely want to Unwrap the Low-Poly version. There is no need to unwrap the High-poly version. Since the Low-poly is the version you will be using for textures, lightmaps, and baking your Normal map (if there is one) you want this to be your primary object to unwrap and make game-ready.
There isn’t a really “automatic” way of doing UVs that will get you good results. In 3Ds max there is Flat mapping which will just break everything apart and throw it within the UV space. This isn’t ideal at all. There is the likely hood that two polygons that are attached will end up on different parts of the UV. Breaking your UVs up manually and marking seams for where the model should broken apart is probably best to solution. It’s not a fast process and is one that should be given a proper amount of time to get just right.
Quixel’s NDo and DDo do not handle UV unwraps. They are simply plugins for Photoshop and must be used with Photoshop. They are for Normal map creation and texture creation.
This is a common dilemma that most users face. Blender is completely free and is capable of doing a lot. To me it can be cumbersome to figure out since I’ve always had 3Ds Max. I’m not sure how Rhino is with it’s modeling but you may run into this as well if it’s similar in any way to Maya or Max. If you were going to try Maya I would suggest the 2015 version as they have completely overhauled a lot of it’s core modeling features and coding. Their unwrap has been greatly improved as well. But as you suggested. Give them a try and figure out what works best for your needs.
When you run into issues with UV unwraps feel free to ask. A lot of my expertise is with 3D modeling for games so I can definitely help out in that respect! There are lot of users who are coming from ArchViz background and other areas that do not require or have a need for UV maps and they are immediately running into a roadblock. Game engines heavily rely on these for real-time efficiency and it’s definitely an art form in its own right.
Don’t worry about having to learn a lot of new programs at once. There are still a lot of things I’m picking up after years of working in some of these programs.
Glad to have on the forums and out from lurking in the shadows!
Tim