How do I clean drains to prevent water from accumulating under passenger seat.

Hello, Water under the passenger seat could be caused by a leaking top, like you mentioned, but more likely it is a clogged evaporator core drain tube. Underneath the vehicle you should find the drain tube for the evaporator core (air conditioning), and that is what allows condensation from the A/C to drain from the vehicle. Between the passenger carpet and the "firewall" is a tube running from the A/C box to the floor. You can either try to clear the clog from underneath the car or by disconnecting the line in the car and running something down the tube. The later method will cause more water to drain into the footwell unless you use a catch can of some kind.