You will find most of what you need for the shuttles in the following file:
SFC3\Assets\Specs\DefaultLoadOut.txt
It is easiest to mess with this if you open it in Microsoft Excel or similar spreadsheet program, but it can also be opened with word pad.
To attempt to add items to the shuttles, it would be best to copy commands from other ships and paste them into the shuttle lines, however, keep in mind there are possible balance issues, i.e. ship mass and capacity. These balance issues can be resolved by altering the following file:
SFC3\Assets\Specs\DefaultCore.txt
This is also best edited with a spreadsheet program. In this file you can change how many shuttles a vessel can hold.
I recommend perusing these guides for particulars on what each value means:
http://starfleetcommand3.filefront.com/files/Starfleet_Command_III/Utilities/Tutorials;1746Finally, to edit conquest mode, seek out this directory:
SFC3\MetaAssets\ServerProfiles\SinglePlayer
The "*.gf" files are text files and can be opened with notepad. What you are looking for may be in MetaMap.gf.
It has been years since I have messed with these files, so I don't want to tell you wrong. Someone else may be able to help you with the next step.