The colors you see in PPU Viewer are stored in PPU Memory at $3F00-$3F1F. Sometimes you can manually change these values in order to change colors on the screen, however sometimes it will be immediately overwritten back, in that case find them in NES Memory in $0000-$07FF and try to change there.
To create a hack with permanent color changes you need to find colors in ROM File (or in any other hex editor) and edit them here. Usually you can simply search for 3 main colors of a palette set, like bytes at $3F11-$3F13 or $3F15-$3F17 from PPU memory. If no luck, try these 3 bytes in a reverse order. If still no luck, then debugging with a Write breakpoint at PPU Memory color address.