Do NOT use SRAM patches unless stated for that ROM on the wiki.If you have a folder named 'GBA' on the root of your sd card, this folder will be opened by default when running GBARunner2.If you are using GBARunner2 with TWiLightMenu on a DSi or 3DS with the SD card, make sure you use the dldi on ARM7 build.NB! If using Twilightmenu++ GBARunner2 will come bundled with it in the sd:/_nds folder.nds file anywhere on your SD card, except for in sd:/_gba. For example, for 3DS pick the one named 'GBARunner2_arm7dldi_ 3ds.nds'.
Pick the one that has your system at the end of the file name. nds file from the link above or the github releases page.
