VX - EDITING GRAPHICS

Hey guys, so I'm fooling around in RPG Maker VX for the first time in god knows how long and I've run into a problem. I'm using the Melody script so I wanted to edit some system graphics like Icons and such but every time I edit something it messes up the transparency and the icons show backgrounds it didn‘t before. Same goes for anything I edit.

I'm using MS paint so maybe that's the problem, or maybe its set to an incorrect file type. I've been trying to correct it but I don't know what I'm doing. Can anyone point me in the right direction? This isn't really my area.

Cheers!