Module files

The module files in Super Smash Bros. Brawl are located in the module folder. All fighters and stages have these files, which have the suffix .rel. For example, st_donkey.rel is the file for 75m.
==Editing stage .rel files ==
You will need a hex editor.
Open the stage module file (of the format st_XXXX.rel) for the stage you want to replace something with. Let's say you want to replace Flat Zone 2 with a stage based on Final Destination. Each module file has a sequence of bytes somewhere in the file that goes like this:
38 A5 00 00 38 80 00 XX
The value of XX is the ID number of the stage, taken from this list:
STCUSTOM (Phantom Wings' code)	00	st_custom[1-9].rel
Battlefield			01	st_battle.rel
Final Destination		02	st_final.rel
Delfino Plaza			03 st_dolpic.rel
Luigi's Mansion			04 st_mansion.rel
Mushroomy Kingdom		05 st_mariopast.rel
Mario Circuit			06 st_kart.rel
75 m				07	st_donkey.rel
Rumble Falls			08	st_jungle.rel
Pirate Ship			09 st_pirates.rel
Norfair				0B st_norfair.rel
Frigate Orpheon			0C st_orpheon.rel
Yoshi's Island (Brawl)		0D st_crayon.rel
Halberd				0E st_halberd.rel
Lylat Cruise			13	st_starfox.rel
Pokémon Stadium 2		14 st_stadium.rel
Spear Pillar			15 st_tengan.rel
Port Town Aero Dive		16 st_fzero.rel
Summit				17	st_ice.rel
Flat Zone 2			18	st_gw.rel
Castle Siege			19	st_emblem.rel
WarioWare Inc.			1C	st_madein.rel
Distant Planet			1D st_earth.rel
Skyworld			1E st_palutena.rel
Mario Bros.			1F	st_famicom.rel
New Pork City			20	st_newpork.rel
Smashville			21 st_village.rel
Shadow Moses Island		22 st_metalgear.rel
Green Hill Zone			23 st_greenhill.rel
PictoChat			24 st_pictchat.rel
Hanenbow			25	st_plankton.rel
ConfigTest			26 st_config.rel
Result				28
Temple				29	st_dxshrine.rel
Yoshi's Island (Melee)		2A	st_dxyorster.rel
Jungle Japes			2B	st_dxgarden.rel
Onett				2C	st_dxonett.rel
Green Greens			2D	st_dxgreens.rel
Pokémon Stadium			2E	st_dxpstadium.rel
Rainbow Cruise			2F	st_dxrcruise.rel
Corneria			30	st_dxcorneria.rel
Big Blue			31	st_dxbigblue.rel
Brinstar			32	st_dxzebes.rel
Bridge of Eldin			33 st_oldin.rel
Homerun				34 st_homerun.rel
Edit				35 st_stageedit.rel
Heal				36 st_heal.rel
OnlineTraining			37	st_otrain.rel
TargetBreak			38 st_tbreak.rel
So in the example, you would want to open st_final.rel search for:
38 A5 00 00 38 80 00 02
You want to replace the XX value with that of the stage you want to replace. So change the string to:
38 A5 00 00 38 80 00 18
Save the file as st_gw.rel. Now you should be able to put a Final Destination-based stage over stages/melee/STGGW.PAC.
For custom stages using Phantom Wings' Custom SSS code, the XX value you should enter is 00.
Also, Smash World Forums user Bero has given us a tool to easily make .rels! http://www.mediafire.com/?zygvyygmwwy
A .rel file to use an OnlineTraining-based stage as a custom stage with Phantom Wings' code can be found here: http://www.mediafire.com/?gkeikwjjqz1
In this file, XX is 00, but you can change it with the method above if you want it to replace a stage already in the game. This .rel file is verified to have no Sandbag. (as far as I know, this is something that PW changed in the .rel, but I might be wrong --User:Libertyernie)