Question about headers

I know that some FFVI patches require a header to put into the game, but I also want to add some other .ips patches and also one or two .bps format patches (like, say, hairy_hen's Retranslation). My question is: What is the exact order for adding the header, putting in both kinds of patches, and removing it?

I use NSRT for adding/removing headers, if that matters. Should I try another program like SNEStuff?