In this case I'm using a CCD camera mounted telescope pointed at the clouds to take solar spectra and was wondering how the telescope being pointed at the clouds through a double gazing (two layer) glass window would affect the spectra, if at all?
you'll need to find the spectral transmissivity of each piece of glass. Most likely they all block UV and large sections of the IR bands. Further, unless you've removed the internal IR filter, your camera won't record any IR. CCDs also cut off in the blue, so no UV will be recorded.
BTW, how are you separating the wavelengths at the camera? Typically one uses a (expensive) grating spectrometer.