So to summarize, just press SELECT + Up/Down to switch between your flashcard and SD content if autobooting, or if you want to keep YSMenu as your main menu and only load TWiLight from there then you'll need to switch to using nds-bootstrap in TWiLight settings on the flashcard, which will maybe lower compatibility but if you're using YSMenu on DS Lite and TWiLight on DSi I think it'd be fine, though they won't use the same save files so probably better to use TWiLight as the autoboot. You probably also have to delete the autoboot line from the YSMenu INI, I think it's in the TTMenu folder.
Thanks, was able to use Select + Up to see my flashcart. I've also removed the line for YSMenu's auto boot, which also worked.
But now, I'm facing a (hopefully final) issue.
To prepare my SD card for a clean install, I format my SD card, then open the "TWiLightMenu-flashcart" and "RetroGameFan Multi Cart Update v7.06" archives. I extract the folders "_nds", "roms", and the files from "Autoboot" folder and "boot.nds" to the root of the SD card. Then from RGF's archive, I extract the folders "Games", "TTMenu", and the file "YSMenu.nds".
So on the root of my SD card, I have: _nds, Games (this is where I store my ROMs and saves), TTMenu, _BOOT_DS.NDS, BOOT.NDS, R4.DAT, TTMenu.dat, YSMenu.nds. I put the SD in my flashcart and it boots up fine. I launch into TWi perfectly, I'm able to boot into YSMenu and launch games and their saves from either YS or TWi. So I take the SD card back out, go to "_nds/nds-bootstrap.ini" and "TTMenu/YSMenu.ini" and delete the auto boot lines. I put the SD card back in, boot the flashcart in my DS Lite. All games boot fine with saves there as well. But when I put it back in my DSi, TWi on the flashcart will load, but no games will. DSi files freeze on the nds-bootstrap loading logo, DS files will freeze with a black screen on top and a white screen on the bottom.
So I tried it a few more times (formatting, transferring files, booting in console) with the same issue. Eventually, I narrowed it down to the first boot will work fine in any system (DS, DSi, 3DS). On second boot, if flashcart is in the DSi, only TWi will boot. Games won't (including TWi's boot.nds and YSMenu.nds), they only freeze. Strangely enough, games installed to SD on my DSi work fine, and no issues in my DS Lite or 3DS - TWi + games work perfectly there. Only games on my flashcart don't when plugged into the DSi. I suspect a TWiLight settings might be to blame for this, but I'm not sure. Any ideas what's going wrong here?
Also, YSMenu and TWi keep re-adding games to autorun without my input. No idea why it happens (TWi will only do it on first boot up, YS will constantly add a new "autorun" line in the config file). I had to make YS autoboot into itself so I had a fighting chance of booting into YSMenu normally lol. Any way to permanently disable auto run? I never want to boot directly into a game.
Edit: figured out if you launch Slot-1 and hold B, it'll boot into YSMenu instead of TWi. Games load fine if I boot them from YSMenu or if I boot into TWi first, albeit they run in DS mode.
Edit 2: I think I figured it out. TWi would boot into TWi on the flashcart a third of the time, but most of the time, it would freeze during loading or I'd get a black screen with four squares - red, yellow, yellow, green. So I folded up a piece of scotch tape hotdog-style, then taped it onto the flashcart label. Haven't had any problems booting into the flashcart since then,