The Ships tab is where it displays any ships that are currently installed, and has options to install new ships, works in a simlar way to the Scripts and Mods tab.
At the top is the Base Mod. The base mod is the mod file that you the ships will be added into. If you use one of the large mods in your game, you can set this as the base mod, then the ships can be appended into the mod. The default is the ":: Current Mod Profile ::" settings. This is a useful setting espcially when used with mod profiles.
The will automatically adjust the base mod to the currently activated profile. So if you have a profile for the XFP mod, then activating the profile will use that mod as the base mod to install ships into.
To change the base mod, just select the drop down list and select one from the list.
Another option is the ":: Standard Game ::". This option is like having no base mod, so the ships will be added onto the standard game. If the mod you use is just a fake patch, like XTM, then you dont need to select the base mod, as the installer can automatically work with any fake patchs. Its only the mods that are in the mods directory and selectable in the X3 Startup screen that need to be set as the base mod.
When you run the game with ships installed, You must select the "PluginManager" mod from the X3 Startup Screen.
Underneath is the ships list, this displays all the ships that are currently installed, and thier current status.
Under the package list you will find the commands to install/uninstall the ships.
If you right click on one of the ships in the list, it will open up the command menu.
The Install Ship, Uninstall Ship and Enable/Disable options are the same as the commands above.