I.e.
Races.esp
Companions.esp (dependent on races)
Do your thing above and make into Races and Companions.esp. (after esmify, etc).
Races and Companions now is dependent on Races and Companions. (this is what it says in the master list).
In Gecko there's an option to "Edit master list" and from there you can remove a master. In your case you would remove the dependancy. Sometimes, this doesn't work. In that case, I always "change" the mod's master to a different one. FOr this, I change it to one I use all the time like OOO, MMM, Warcry, or Frans.
BTW, I've seen it come up again and again in this thread, but the "edit Master list" can also reorder the masters of the mod rather easily. When it's "orange" in the Wrye Bash, the master's list of that merger is simply out of order as they appear in your own load order. Let's say you've got a mod dependant on:
Oblivion.esm
MartsMonsterMod.esp
OblivionWarcry.esp
And when you merge them it shows like this in the master list:
Oblivion.esm
OblivionWarcry.esp
MartsMonsterMod.esm
The mod will now be orange. Why? Because in a proper load order Mart's Monster Mod.esm will be BEFORE OblivionWarcry. So to solve this, go to edit master list for this mod and simply move up MartsMonstermod.esm one space which will cause warcry to go down one space. You can do the same just moving Warcry down one space.
One thing I stress to be careful about. If you're already in a game, and you merge 2 mods you've been using, then change the name of the merged plugin to one of those, the one who you DIDN't change the name to's items will disappear from your inventory. You can simply go back and get it again. Here's an example:
1) Merge 2 bag mods. Wondrous Inventory and Bag of Holding. Make a MergedPlugin.esp.
2) In order for BOSS to keep reading it and auto place it in proper load order, you change the name to "bag of holding"(since Wondrous Inventory isn't in the Boss list yet)
3) If you already HAD Wondrous Inventory, it's now gone from your inventory until you go back and pick it up again.
4) If not careful(i.e. removing all your stuff Inside Wondrous Inventory) you may lose all the items it had in it.
The thing is even if you just kept the name "mergedplugin.esp", and you had both items, BOTH of them lost all their stuff. This is just something minor to watch out for.
I did this once myself, the wrong thing that is. However, I was pretty lucky as when I went back and picked up Wondrous Inventory again, it had all the items still in it.
Another thing if this happens and you notice it as soon as you log on..."Oops". Then simply DO NOT SAVE. Go back, Uncheck the merged plugin, bring back the original mods and check them.
A good rule of thumb is to always use the Wrye Bash "hide" feature instead of deleting. When you delete it, all you're deleting is the esp. THe meshes, textures, sound,etc. are still in your data folder. So when you "unhide" them, it'll still work just fine.
Another thing about "cleaning". Gecko is too slow to clean your mods properly(however it gives it a good going over if merged) . Heck, we've GOT to have time to play,lol. Arthmoor has recommended TES4Edit and so do I. If you do a "mass cleaning" it may take up to 30 minutes depending on how many mods you have with Edit, but it's still faster.