One thing to consider is the internet makes drawings/layouts really easy to find ideas now.
You can also find design programs too if you want to make really complex layouts, my parents designed their house in some 3D modeling program.
I think the biggest thing that I would consider is how many places you've lived so far. Everyone has things they "want" but often these change over time, or turn out to not to really matter, or otherwise change their minds on once they've lived in a place. It's not clear how old you and your fiancee are but something to consider. Particularly house size - do you want to design a 2k sq/ft finished house plus a 1k basement only to find out you don't want a house that big? Building a bigger than you want place will kill most of the gains you find here.
Regarding the question, I think it's fascinating because I'd love to do something like this some day. Once you decide if you are designing it or not, the next step is compulsively researching things. Talk to your local utility companies, ours does a free energy assessment and I'd expect that those people would be more than happy to talk through ideas.
Thanks for the reply. I was thinking a little less about how the rooms would be laid out and more about window types and sizes, facing for maximum natural light and heating exposure. Insulation to make the house the more efficient. Things like that.
Room layout has a huge impact on this, though, because how your rooms are laid out in your house affects their natural lighting and heating exposure. For example, if you live in Ohio, having many north and northeast facing windows under
large overhangs (a great tool for efficiency) means you can get optimal natural heating in the winter and light year round. So designing the layout of your house to face in such a way to maximize the potential means you can better optimize this.
Along those lines, if you have the ability to build in or surrounded by timber, you can get built in benefit of summer shade which can save a considerable amount of direct sunlight in the summer. This can be substantial savings in AC. You could also setup a solar array on the ground facing an ideal direction if you have an acreage, so something to consider.
I would definitely do geothermal, because I really like the idea of being more "off the grid" and since we're designing a dream home on many acres it'd be easy to do geothermal. Make sure you have a way to setup a generator or battery storage somehow (I think this is actually becoming more economically feasible, particularly if you have a solar array, though I've not looked recently).
Two above ground stories strikes me as likely to be less efficient. Can you do a ranch with a walkout instead of another above ground story? This will be more efficient but only you can answer how important an unfinished basement is for your plans.
How far will you be from a town? What do you plan on doing as far as gardening goes? One thing to consider is if you end up wanting to store lots of stuff in extra refrigerators or freezers to have a place for them. My wife and I love doing this and our current house doesn't have a great spot to put extra chest freezers/etc. Consider the lifestyle you want to live and make sure you can do so in your house. But also realistically consider it.
When building you should do a ICF house (insulating concrete form). Bad if you want to start taking out exterior walls and changing the layout of your house but great if you want to build it from scratch to be more efficient. Huge perks from an efficiency perspective. As well as offering some security against inclement weather, bugs/pests, and kids punching holes in the wall ;-) ICF by design has a ton better efficiency than wood framed, because wood is a poor insulator (take a thermal camera sometime in the dead of winter throughout your house, you will trivially see studs because of how much cooler they will be than the insulation between them) and because it's a much more airtight setup.
You may consider building either a drainage pond or capture system for rainwater off your roof, depending on whether you care about this.
There are lots of insulation tips and tricks. When designing from scratch you can do a lot along these lines. ICF helps with this but you can obviously insulate a lot of things still. Likewise you can get decent windows, which range all over spectrums from junk to super-ridiculous.
Consider how your doorways work. Do you have a frontdoor which opens into a great room? It'll be more prone to letting out heat in the winter and cool air in summer. A more typical mudroom setup, particularly if it has doors on the other side, can be helpful here.
Build ceiling fans into your rooms. Consider putting a whole house attic fan in your house.
Make sure your HVAC is appropriate. Don't overbuild it (particularly if you get ICF, which will reduce the needs of it). Don't under build it. Make sure your HVAC is setup right and you will save a ton of energy. Most houses have rooms which are +/- 10 degrees from the rest of the house, which means if anyone is in them, it's a pain. Try to make your HVAC work well (which isn't easy).
You might even want a woodburning stove or fireplace if you are going to be living on an acreage with timber. As long as you can efficiently insulate this if you are not using it, you can trade your sweat equity for free heating.
With ICF you can find a lot of related efficiency tips online, particularly as this matures.
Really, don't underestimate the effect that intelligent layouts and how the house faces factoring into this.
I guess I've thought about this a lot over the years. Can you tell? :-)