Hmm, this may take a bit.

The diplomacy and Entrenchment expansions are basically mods placed in the root directory. The usual root is...

C:\Program Files\Stardock\Sins of a Solar Empire

The game first looks at the original base game files and goes up from there. So if you are playing diplomacy it checks the base game then entrenchment then diplomacy for newer files.

If you enabled multiple mods in diplomacy it checks them from bottom up so the top one will override a lower one. 

So lets say you want a new CapitalShip_TechBattleship which is the TEC KOL Capitalship in the new diplomacy mod.

Lets say you have 3 mods enabled in diplomacy all with different versions of the KOL

The game 1st checks the base game (found original KOL, lets say ver1) then entrenchment and diplomacy (no newer KOLs here). Then the lowest enabled mod (found a newer KOL lets say ver2) then the next mod up (found another KOL, lets say ver3) then the top mod (found another KOL lets say ver4.) The game will ues ver4 of the KOL because it overrides all lower mods and base game.

Keep the same folder structure as the game but unlike the game install folder where it has Entrenchment and Diplomacy separate folders your mod will not need this. Lets say you modify files from the "GameInfo" folders from all three games. They will go into 1 GameInfo folder in your NewMod folder.

[Tutorial] Placing Mods

harpos converted reference files are a great place to start. Get all three sets if your modding for diplomacy. the diplomacy reference files only have what was changed for diplomacy, same for entrenchment. So 1st look for the files you want to modify in diplomacy then entrenchment then org game. Place all the files you modify into 1 mod folder in the folder there from eg GameInfo.

[Tutorials] 3D Modeling, Texturing, Importing & Converting

What are you not understanding then? If you aren't adding new factions/races then it's still fairly straight forward and follows similar modding rules as Entrenchment. If you need help with Diplomacy Pacts with new factions/races I can help answer any questions you might have.

Just add the Diplo files to the manifests and remember the following:

Frigates have an "allegianceDecreasePerRoundtrip" line added to their entity file, add that to any frigate .entity files in your mod.

Player .entity files have the envoy frigate, diplomacy researches and relationship modifiers added. (possibly more, unless you have a 5+ race mod just copy the Diplomacy player entities and repeat any changes you made)

Some researches were moved to the Diplomacy research tree, move them in your mod.

Pirates got several researches added, so if you modded them you need to add the Diplo changes (if you want them) If you didn't mod them the game will automatically use the Diplomacy files

Luckily there was no change to the syntax for Abilities/Buffs/Capships/Starbases, so you don't need to rework those.