A good start is Schumi's FAQ.
Assuming you use 2.6, as 2.6a is not legally available - and hasn't been for what is about a year now -, you'll need to set the savetype under Options->Emulation setup->NDS cartridge backup media to whatever the game in question needs.
To find that out, go to Advanscene (link in my sig) and quick-search the game. Then, divide the numerical value shown there by 8 and you'll get the No$ savetype. Also note that the Flash savetypes are given as Mb on the page; multiply them by 1024 first to get to kb.
FF4 is known to corrupt the save if booted with the wrong savetype, so start No$ with another game to be sure.
You won't need to use it for either of those games, but NGZoom is a REALLY useful utility that zooms the No$ window to fullscreen size and fixes some emulation issues. Get it and extract it to your No$ folder. If you run it, it will auto-start No$ with the altered options.