it will affect every format you open in it, but with KSM, you can have both nickel and koreader on one device.
installation instructions are here:
https://github.com/koreader/koreader...n-Kobo-devices
you have to use version 622 and higher from nightly builds, only those work on KA1:
http://hal9k.ifsc.usp.br/koreader/
btw kindle comic converter is useless and wont solve anything, it will only convert the images to screen resolution of your desired device, but the borders of white space will still be there.