If you have a mostly empty 4GB SD it should be enough to fit Pokemon Y twice – as CIA and installed. This is why you should check what else is on the SD with a computer and why I asked you to build a temporary setup by formatting the SD [↑See above↑] (after backing up the current SD status).I deleted them through the 3ds itself and how do I do network installation?
Ah crap ok so I found out that to install a .cia file you need to have double the space on the SD card and Pokemon Y is 1.7gb so I won't be able to download it hah crying time
To work around that “I need twice the space!” issue (which is quite bad on very small SD), you can use a (Windows) software called Boop and the [Remote Install → Receive URLs from Network] feature of FBI.