Snes9x help

Okay. So...

I have Snes9x downloaded and installed on my homebrew channel. I also have games on there that run properly ( mostly at least ). However my problem lies within actually saving the data. I tried first on my Earthbound file, and found that I have to start a new game again, luckily I hadn't gotten too far. Then I checked Crono Trigger, just in case something messed up with Earthbound. I checked to see if the directory to where it was being saved was right, but I'm not entirely sure how to accurately do so. I'm not even entirely emulation savvy. I appreciate any help from anyone who might be able to point me in the right direction of how to save my SNES games. Thank you very much!

The directory that contains your save files should be
SD:/snes9xGX/saves.

I assume you are talking about normal in-game saving and not the save-state function. If so:
Go into snes9xGX's Saving and Loading settings and check to see if auto-load and auto-save are on for SRAM.

Yeah, I checked to see if the auto save was on, and as I stated before, I'm not entirely savvy with this sort of thing, but I figured SRAM was the correct option. Nothing was saved though, I have the file, but nothing is there. Does it matter if the snes9xgx/saves is in a SNES9xGX main folder on the SD? cause I have the apps folder with my snes9xGX, Wii64, and vgba. I was confused because my vgba has both the roms and saves inside the apps folder and it saves fine, however the same is not true for my snes. Sorry if I'm being a pain, I really appreciate all the help.

If the folder Snes9xGX is looking for doesn't exist, then it might not save into it.
In the Snes9xGX Saving and Loading settings, you can tell it where to look for files. Arrange the folder structure on your SD card however you like and then inform Snes9xGX through its settings.