On a 5th generation Honda Civic the thermostat housing is located on the back of the engine, bolted to the transmission end of the head.
Follow the lower radiator hose to where it connects to the engine and that is the correct place.
This generation of Honda uses a gasket on the housing, not sealant, be sure to orient the thermostat with the bypass pin up and use a new gasket.
Be sure to top off your coolant with 50/50 distilled water antifreeze mix.
And always bleed the system of air bubbles, there is usually a bleed nipple located for easy access, Hondas are very picky about air bubbles.