Hello there...
i have some questions and im on 9.2 sysnand on O3DS so:
1)How can i play GBA games using the injection method
2)Why when i keep installing custom themes they are not there? It worked the first time (.cia)
3)I am playing Rutile Ruby but i cant go online. Can i update the game without losing its edits?
4)Can someone guide me through number 1?
I'd recommend reading and learning about CFW first, and think about using emuNAND. Regardless, you'll end up installing the GBA .cias to at least sysNAND, but you can't do that without a .cia installer. Which you might need to install to your sysNAND, but without a CFW patching some things on the fly, that won't work. FBI comes in both a .3dsx and a .cia, but I don't know what permissions the ninjahax2.5 grants, so we're back at CFW and emuNAND.
Once you've got that all figured out, look here for making your own GBA VC .cias and patching the AGB_FIRM:
https://gbatemp.net/threads/release-agb_firm-signature-patcher-gba-rom-converter.390313/ This here is another reason to look into using emuNAND, as you'd have to patch the AGB_FIRM (unless you're using a CFW that patches that on the fly, but it didn't work for me when I used one that did until I installed a patched AGB_FIRM). The less you have to mess with your sysNAND, the better. To note, too, you don't always have to make your own; .cias of GBA VC injects exist but you'll have to look on that iso site or others because they contain ROMs in them.
No idea about the custom theme thing; I've always just used either the menuhax installer or CHMM2.
Rutile Ruby and Star Sapphire require you to have no updates installed, so I doubt it.
I've given you a good link there, but as for CFW and emuNAND setup, there are a couple of threads out there. I recommend using rxTools if you're not sure which CFW to use.
This tutorial is the one I used, but at the time it had links for rxTools. It has CakesFTW, which will get you started at least. Plus you might end up liking CakesFTW anyways since it has a neat patch system. At any rate, search around here ReiNAND, Pasta, rxTools, and CakesFTW at least so you can get an idea of what you'd want in a CFW. After getting things set up, read about those and go from there.