Yeah, that should work fine as long as you follow everything correctly. I do pretty much the same thing, but I use "hdd raw copy tool" instead of win32 disk imager, because it makes slightly compressed images.
I think that you will have to backup your SD image before writing a different one though, if you want to keep your saves, because I don't think there is any other way to backup saves from 9.6 emunand (maybe the official nintendo tool works, or maybe backing up the "Nintendo 3DS" folder from your SD works, but I personally would just stick with backing up the full SD image before writing a different one).
edit: also, no need for formatting to switch your 4.5 cfw to an emunand. just backup your 4.5 cfw SD, then boot into your 4.5 cfw on your 3DS and delete the non legit .cias (if you have any
) and then install the legit .cias you want to use on 9.6 emunand, then convert your cfw "rednand" to a gw emunand (I use hXD for this, if you google you should be able to find tutorials, especially on some iso site. basically you need to copy everything from offset 200 up until the end of your emunand - the length of your emunand can be determined by doing a nand dump with gw launcher). Once you have your legit .cias installed and you have converted to a regular emunand, you can update with rxTools in Rx-E mode and play your .cias once you get to 9.6.
NOTE: smash bros and MH4 don't seem to work on rxTools emunand right now, so don't get your hopes up for playing those just yet. Hopefully roxas can update rxTools to fix that, but I don't know if it's possible.