Alex,

I'm assuming the curtain wall system would be installed as an over-clad
to the existing punched windows, essentially creating a double-wall
facade of sorts? If not, simply create different window types in
eQuest, one for the curtain wall IGU and one for the single pane window.
Existing opaque walls and curtain wall spandrel panels are created as
different opaque wall types.

Otherwise, you might consider searching the lists for double-wall
facades, but as a first step, I would approximate the system as follows:

Create a triple-glazed IGU for sections of the wall with the IGU and
existing single-pane windows;
Create a new opaque wall type for section of the wall with the IGU and
existing opaque wall with a blended U-value.
Something like this (pardon the crude MS Paint):

You might not get the full impact of the continuous air gap between the
two facades, but you could play around with the width of that air gap to
either make the convective losses more or less pronounced depending on
what your system actually looks like. I believe that after an inch, the
convective losses between the two panes of glass begin to outweigh the
insulating benefit of the air.

You should pay close attention to how the curtain wall is fixed to the
building to properly account for thermal bridging of framing elements.
I like Natural Resources Canada's EE4 simulation tool for creating
custom assemblies. It's free and simple to use:
http://canmetenergy-canmetenergie.nrcan-rncan.gc.ca/eng/software_tools/e
e4.html

However, this method doesn't consider the interactions of the two
cladding systems when it comes to solar gains and visible light
transmittance very well. But if your project is in a cold climate,
thermal losses would be more important which I think this method
accounts for reasonably well.

BTW, what does this look like in elevation? Are there strips of
spandrel panels? You'll need to consider framing effects of horizontal
mullions too.

Any thoughts from the rest of the group?

Cheers,

Luka Matutinovic, B.A.Sc., LEED(r) AP