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Just combine both into one signle file and that's it - no header, the emulators should be able to read the internal header, and they will automatically use LoROM or HiROM depending on where you place the header (I belive it's at $00:7FF0 for LoROM and $00:FFFF0 for HiROM).
Some SNES ROMs have a 512-byte header, but I guess it's useless and have no purpose, I'm not too sure though. Maybe it's used for games which uses special mappers ?
The internal "header" should be at the correct offset already in those dumps.
The extra 512-byte header is useless except if you're planning to play the ROM on a Super Wild Card or some other floppy-based copier, so there's no need to add it.