How do I pull up D1-D6 using 10k ohm resistors?
Typical Atmel AVR inputs can “float” when left open, that is, may drift high or low.  The idea of a pullup or pulldown resistor is to give an otherwise-open input a definite value – high if pulled up, low if pulled down.

The values of pullup and pulldown resistor values are a tradeoff:   You can use high values to minimize the current that a sensor device must overcome when it switches values, and to minimize power loss in a battery-powered device.  Or you can use low values to get faster switching when you release the input.  

There are built-in pullup resistors on most AVR inputs.  (But A6 and A7 on some models of ATmega328's don't have pullups.)  To use a built-in pullup, initialize the input pin with (for example) pinMode(mypin, INPUT_PULLUP) instead of pinMode(mypin, INPUT).

To sense the state of a simple normally-open switch, you would connect one side of the switch to an input, and the other side to ground.  Initialize the pin to be a pulled-up input: eg, pinMode(mypin, INPUT_PULLUP).  Regard the switch as not-pushed when digitalRead() shows HIGH, and  pushed when it shows LOW.

If you really want to use external pullup resistors, connect the switch as above – one side to ground, one side to a pin – and connect a resistor between +5 V and the pin.  That is, one end of a resistor and one side of a switch will connect to the input pin.  In this case, use either INPUT or INPUT_PULLUP as the pinMode setting; it makes no big difference because the internal pullup resistor has a fairly high value, eg 40 KΩ.