I just happen to have a power window relay sitting on my desk while reading this, so hopefully this helps. Your underhood PW circuit will have two components to it - a circuit breaker that's designed to trip over 20A and reset when it cools back down, and a relay that switches power on and off to the power window circuit when the key is on. (Note: I have an early '63, your wiring might have some slight differences.)
The Circuit Breaker
Like you guessed, the two-wire box under the relay is a circuit breaker. One side connects to the starter solenoid so it has a good, high-amp source of B+, and the other side connects to the PW relay. It should look something like this.
The Power Window Relay
Every relay is going to have at least four connections - one to supply power and one to ground the relay coil, one that supplies the higher-power source that needs to be switched by the relay, and one that is the output of the relay to the circuit being switched. I've attached pictures of (from what I understand, original) relay here. The four connections are:
IGN is the source of key-on power that energizes the relay coil. On my '63 this is connected to the voltage regulator about a foot away and is yellow with a black stripe. It's my understanding that later Avantis changed this so the power window relay is energized when the key is in 'accessory' instead of just 'on', so your '64 may be different
Ground is done through the frame of the relay. Being a fiberglass body, there will be a white wire connected to the bracket that mounts the relay, and that white wire is what provides the ground for the relay coil. With both IGN and Ground connected, you can make the relay energize and click - you'll hear the coil sucking the contacts closed inside the relay can
B is the high-amp power source that the relay is switching. The other side of the circuit breaker is what supplies power to this terminal. On my car this is black.
W is output from the relay to the power window circuit of the car. This is also black on my car.
So for any of those replacement relays posted, the three terminals will be IGN, B, and W. The mounting bracket of any of those relays will be the ground for the relay coil. Hopefully the replacement relays come with a diagram showing the pinouts, so you can tell which is the coil positive connection and which two will be the switched terminals.
Alternatively, you can find some nice Bosch-style relays that can switch up to 30A and use a standardized pin-out, which has become the de facto standard for automotive relays for the last 40 years. If you do, the wiring for those I've attached also.
Best of luck!