know its been asked millions of times

Good question, actually.

You'll need to place a mod into the version-specific mod folder.  So, for any Diplomacy mod, you would place the files into the 1.011 folder as you suggested.  For an Entrenchment mod, you'd place them into 1.051, and then you'd obviously do likewise for an original Sins mod.

Remember that a mod placed into any one of these folders only affects the version of the game that it's meant for.

is kinda wanna modify stuff from the pww sins and make it useable in diplomacy version of the game

I'm not sure exactly what you're referring to, but the amount of work involved in that kind of port will depend on the content you want to use and the organization of the original.  For instance, in SOA 2, we had originally renamed all of our files to reflect Star Trek-specific content.  To better adapt to constant patches, however, we switched back to using the stock game's naming conventions while using trek-specific names only for our 4th and 5th races. 

If file name changes have been made, you'll have to make a lot of small adjustments in nearly every text file.  If it's just some minor alterations within entity files and whatnot, then you simply have a few extra lines to add ("usesFighterAttack" and "allegianceDecreasePerRoundtrip" come to mind).  Text files with different names or that are in addition to the standard compliment of files must also be added to the manifest files, otherwise the game won't recognize and load them.  This includes entity, brush, color, and window files.

Things like textures, meshes, and particle effects just need to be put into the appropriate subfolder to function correctly.

sorry just wanna make number changes to tech's (ie cheat!)    without actually cheating (since i actually only play single player!) 

do i put all the research subjects into 1 folder for a mod or do i have to separate them into folders for each game            ie. under the mod folder make a gameinfo folder for sins, entrenchment and diplomacy or just put them under the diplomacy folder

If you make a mod for diplomacy you will want to add the files you modify from original sins, entrenchment and diplomacy into 1 NewMod folder in...

C:\Documents and Settings\user\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Mods-Diplomacy v1.011\NewMod

So if the files you want to modify are not in Diplomacy, look in Entrenchment, if not there look in Org Sins but put them in the 1 NewMod folder keeping the same directory structure.

Your NewMod folder does not need to look the the install dir with the seperate Ent and Dip folders, all gameinfo files into 1 folder