The sky+ treats the rom as an original game you get any updates from the eshop, you could update your 3ds to the newest version and it will still work. You will need a private header to play online but I guess becuase you have a gate way you already have a header
Getting the games to play
all you have to do is put the .bin and your game into the root of your card. You get the file from the sky page
Your done with getting the games to play
For online continue
Settings file set up
After you start up a game a files on the root of your sd card will be created. That's your overall settings. open it and change "CREATE_PER_GAME_SETTINGS=x" to "CREATE_PER_GAME_SETTINGS=1"
You are now done with the setting file save and exit. What this does is it makes it that every time you start up a game on the 3ds it will create a cfg file for it.
CFG file set up ( private header )
After you did the settings file insert the sd back into the sky and into the 3ds. Start up the game and that should create a cfg file. If you want to edit multiple games you're going to have to start up the game first in order for it to create the cfg file for it. after that go back to computer and open that cfg file. It should look like this. Your numbers will obviously be different
CART_ID=YYXXXXX <- The YY is your cart manufacturer you will change that to whatever you're is. DONT TOUCH THE OTHER NUMBER
ENC_TYPE=00000000
ENC_SEED=66E19DD1F3D0FF3AC68781F932189DEE
FLASH_ID=62261100
GAMESAVE_KEY=HHHHHHHHHHHHHHHHHHHHH <- this is the place that you put your private header. REPLACE WHATEVR NUMBERS ARE IN THE SPOT WITH YOUR HEADER.
What's my cart ID?
So you're probably wondering how do I know what my car manufacturer is. Well that's just going to be trail and error. It would be any of the following
C2 = Macronix
AE= OKI Semiconductor
45 = SanDisk
All you have to do is replace the first two digits in the cart ID with C2 or AE or 45. It's represented YY above. Save and close and your done. You have to replace the private header and the manufacturer ID for every CFG file that you want to go online with.