Basically enable Texture Dump on the plugin, (Under the menu Texture Filters)
this will create a directory for your game, eg.
C:\Games\1964\099\Plugin\texture_dump\ZELDA MAJORA'S MASK
within this, all textures that have been displayed so far in the game will be dumped.
You can edit these, but ensure the new file size is either 1x, 2x, 3x or 4x the original size of the texture.
Once edited place the images (WITH THE ORIGINAL FILE NAMES) in a new folder in the plugins directory, eg.
C:\Games\1964\099\Plugin\hires_texture\ZELDA MAJORA'S MASK
within this you can organise textures into groups
C:\Games\1964\099\Plugin\hires_texture\ZELDA MAJORA'S MASK\Main Menu
C:\Games\1964\099\Plugin\hires_texture\ZELDA MAJORA'S MASK\Loading Sequence
Now in order to see your new textures enable "load hi-res textures if available" under the same menu
and thats about it really, as far as i know. But it is INCREDIBLY tedious work and I always give up =p
Edit: seems the forum hates the word zelda, =/