1. where are rom saves located? do they save on the SD in the 3ds or on the microsd in the gateway?
While playing, the save is stored inside the Flashcart's own save chipset. In order to backup the flashcart's chipset content to the 3DS SD Card, you need to exit your game using Home > exit (X) > Accept (A).
If you change your game (in microSD card), it will restore the latest save file for that game into the flashcart and overwrite the existing content.
If you are playing the same game than the last time, it will use the save located in the Flashcart and will not restore the save from the SD card. (meaning, if you let the battery die, don't worry, it will not overwrite your last progress with an old backup, as long as you don't change your game after letting the battery die/power down the console/Format SD card)
2. if im playing a retail cart of Zelda using emuNAND, then later update the real firmware on my 3ds will the save file still work on the Zelda cart or will it get erased/corrupted?
Zelda is using the new Save encryption method, therefore if you play that game on EmuNAND Classic it will not use the same encryption than RealNAND6.0.0+, and you will loose your progress. (same problem is yuo start playing on Real NAND and later put it on EmuNAND Classic).
3. if im playing an eshop purchased version of Zelda using emuNAND, then later update the real firmware on my 3ds will the save file still work or will it get erased/corrupted?
I think games/applications downloaded using EmuNAND don't launch on RealNAND. You see the icons, but can't launch them. If you go to Data Management in your RealNAND Settings they will be deleted.
Game updates/patches downloaded on EmuNAND are working on RealNAND. They will be deleted if you go to DataManagement too.
4. if I buy Mario kart from the eshop using emuNAND will it show up on my 4.4 firmware 3ds when im not using gateway? can it be played without using the gateway?(I assume the game is patched when downloaded) will going back and forth playing the game using emunand then playing it without gateway corrupt/erase the save file?
It will show up. You can't play it without EmuNAND. I don't know about playing it in Gateway mode without EmuNAND (Someone has to test and report!).
5. what triggers the 3ds to check for or download a firmware update? is it the game/app firmware requirement or will it still check if I go online with Mario kart on 4.4 though it doesn't need newer firmware to run? will it try to update firmware when in standby?
The 3DS periodically check for an update. if Wifi is enabled, it will download the new update. It will also download when in Standby, and when you enable streetpass (even without any network settings).
6. does using parental controls guarantee the 3ds will never update the firmware and which option do you restrict?
I think that restriction was removed. Someone can confirm?