
If you are using a 3DS family console, you can install custom skins using Universal-Updater. Skins for the R4 Original theme go in sd:\_nds\TWiLightMenu\r4menu\themes\.Skins for the Nintendo 3DS theme go in sd:\_nds\TWiLightMenu\3dsmenu\themes\.Skins for the Nintendo DSi theme go in sd:\_nds\TWiLightMenu\dsimenu\themes\.Once you have acquired a custom skin, you can install it by placing its folder on the appropiate path, which depends on what theme the skin is made for. The Homebrew Launcher, Sega Saturn and Game Boy Color themes are not customizable. You can also make a custom skin for the Nintendo 3DS and Nintendo DSi themes on your own by following this guide. I believe you can tweak certain things via godmode9 - such as screen brightness - using the open_agb method, but it's pretty esoteric to the layman, and not at all user/n00b-friendly.Custom skins for themes can be acquired from the official skins site, which houses serveral community-made skins ready to apply. However, this method is severely lacking in options/features/customization. There are two ways you can do this: Either "injecting" the ROMs on your 3DS as Virtual Console games/apps on your 3DS Home Menu using a forwarder program such as "New Super Ultimate Injector", or downloading "open_agb_firm", which can then be accessed by holding start while booting/turning on your hacked 3DS, and selecting it from the Luma Chainloader. I would say the best option for playing GBA on 3DS would be using Nintendo's own built-in, native GBA emulation on 3DS, as it isn't really emulation at all, and all the ROMs run perfectly. But it does have fairly robust features and customization options. But it's not perfect, and I would say it's honestly more useful for GB/GBC emulation than the GBA itself. MGBA is fairly serviceable, for the most part.

I also found GBA Runner to be a pretty shoddy emulator. However, I wouldn't recommend TWiLight Menu/GBA Runner as the optimal way/emulator to play GBA games on your 3DS, simply because TWiLight Menu essentially turns your 3DS into a DS, and the DS has a pretty low screen resolution. I don't have any better advice than what has already been given on the corrupted folder/SD card front.
