1) TREman is called TRE Manager, and it's for managing the .tre files. TRE files are sort of like ZIP files - they are compressed files that store all the files the game needs to run like ships, missions, comms, etc etc.
For a detailed tutorial on using it, see my post here:
http://www.crius.net/zone/showpost.php?p=340181&postcount=12
EDIT: You have to turn off UAE if you're using Windows VISTA to get Treman to work. If you're not, don't worry about it.
2) WCPedit is a much more useful tool - it's (essentially) a ship swapper that lets you change two ships for each other. I believe it needs to be used in conjunction with TREman to unpack the TRE file containing the ships, but I may be wrong about this. WCPedit also lets you change the default game value for things like speed, guns, missiles, and armament. This can be fun, but can also ruin the game so use it carefully.
WCPedit will work with Standoff ships and Missions, but you will have to add them to the WCPedit program first. There aren't really any tutorials explaining how to use WCPedit, but then, you shouldn't need them anyway unless you're creating you're own ship that uses an existing ships framework but has seperate stats for a custom missions.
(Anymore discussion about this should probably be taken to another thread, since it's more then slightly off topic and will have a better chance of getting answered if it's in the Fan Projects & Editing forum.)