I'd like to change the armor that the solders from encave commander mod are wearing to a custum one from another mod, I've tried with few differnt clothing mods in both cases this is what happens. I change the NPC inventory and I save the plug in, but when I either reopen the mod in the geck or start the game with the plug in actvated the new armor is missing from the inventory. I would also like to add that I have given the NPCs custom weapons as well from an other mod, but I've have no problems with that. Is there some geck setting I have to change? Thanks in advace

My guess.

You cannot use an ESP (Elder Scrolls Plugin) in your mod, which is itself an ESP.

But your mod can use ESM (Elder Scrolls Master) files for resources.

That makes sense actually, the weapons mod is an ESM, are there any faqs for combining ESPs (ie combining the two collections of armor/clothes in to one esp file) and how to convert that into a ESM?

FO3Edit will allow you to merge esps and then set the ESM bit on the result. What I do is merge the two into a third (new) esp (copy as deep override). The two original esps are flagged as Masters in the new esp. Save and re-open the New esp with FO3Edit. You will notice that the two old ones load too. They need to load before the new esp, so you may need to adjust their order with FOMM. Then remove the two masters from the new esp (you want to leave fallout3.esm)! Close FO3edit and save. Reopen the new esp with Geck and check for errors that pop up. If the errors were in the original mod you will see them here also. Some don't matter too much. You should see all the records in your new esp that came from the other two esps. Save the plugin again and exit. Open the new plugin with FO3Edit. You will notice the old esp's no longer load. Click the ESM flag in your new esp to enable it, then exit/save. Rename your esp to an esm. Set it's load order in FOMM. Make sure you take the old esps out of the load order - you don't need them anymore. Keep in mind that if you have a game save that included items from the old esp's, you will LOSE them. So only do this when you are ready.
FO3Edit can be obtained here:
http://www.fallout3nexus.com/downloads/file.php?id=637
A very well written guide that explains everything I just described with screenshots can be obtained here:
http://fallout3nexus.com/downloads/file.php?id=8629