so good job with the sd card ^^ one less thing to do then.
cia updates should be marked as that. but even if the file is bigger as the game, doesnt mean it can be the game with dlc. i dont even know if a cia game is bundled with updates. but remember you can use the 3ds for game updates, so you just download and install the game cias. when connected with the internet, it asks to download the newest update for the game. if by any chance you dont want to or cant connect the 3ds to the internet, you have to download the updates too.
after installation of the game, the .sav files are located from the root of the SD Card:
X:\Nintendo 3DS\"long combination of numbers and letters"\"another long combination of numbers and letters"\title
from there on are many folders. they are named after the title ids. i attached a screenshot for an example.
for more information, i found a reddit thread:
https://www.reddit.com/r/3DS/comments/4awyuo
for emulators, maybe try RetroArch. or if its too complicated to use and still not what you are searching for, try: New Super Ultimate Injector for 3DS
with the double amount of storage, either you can install and delete the cias and you back up those cias on the computer, or there could be another method to use ftp or something to install cias from your pc. not sure if you need it.
still, with the sav files its complicated. if you need any help with that, ask again ^^
and about the different sizes, games can be trimmed so the size gets smaller but you can still install the cias, or they are decrypted for citra emulator so you can use them with the emulator which seems to make the file smaller too.