It's fun reading data sheets and getting all down on the chip, but the purpose of the library is to relieve the user from the need to understand the underlying details of the chip.
The library used provides reasonable analogs for digitalRead(), digitslWrite() and pinMode(), with the only significant difference being that the library defaults to internal pull-ups enabled.
With a real pull-up added, or not (internal still enabled) an open pin will read HIGH, that pin with 5 volts on it will read HIGH, and that pin presented with 0 volts will read LOW, if the grounding is stronger than the pull-up. A switch (shortest circuit) will be strong enough.
If you want pulled down pins, just set the pin mode off using pinMode() and wire a pulldown resistor between the pin and ground as usual.
Can you please post a copy of your circuit, a picture of a hand drawn circuit in jpg, png?
Hand drawn and photographed is perfectly acceptable.
Please include ALL hardware, power supplies, component names and pin labels.