You'll install new ships into Inferno\Mods\
When you add a 'mod- mods' commandline the new ships will appear at the bottom of the existing ship list in FRED as they use modular tables, you won't be required to edit the ships.tbl at all. This prevents patching issues as these mods do not effect the existing ships.tbl entries and a ships.tbl patch won't effect the modular tables.
Removing the -mod commandline turns the extra ships off.
The only time a seperate mod folder would be needed would be for full larger user campaigns with mutiple files, which should still use modular tables and not edit the main table file.