3 year late post, I know, but your screen is wavy because you are using an emulator. The actual game(including Wii U Virtual Console- which I use now) does not shake. I used to use an emulator to test out certain things, which is precisely how I know this. It shouldn't be any concern-- It is mainly due to the game's coding being rather difficult to work with on emulators, it took a few years for people to get the Golden Sun games running on VBA without lag.
As for puzzle help, well, since I'm only posting this for the sake of helping others in future, I'd suggest looking up a walkthrough for the specific area you're at, then scrolling until you find the exact puzzle you're stuck on, and follow the instructions. Personally I've only ever used them in this game for Djinn and Summon Tablet locations, but then again I'm fairly good with these types of puzzles, I can see why some can get stuck. No shame in checking a walkthrough ^-^