rm65453:
I am using diagram one for the switches so I think i am good.
No, it is not really good.
Diagram three is the preferred version because it is in general not a good idea to have the 5V line itself going to any component that it does not need to and especially where that involves going to external wiring - as may often be the case with switches or sensors - due to the consequences of an accidental short to ground. If a switch or sensor line is shorted to ground where it switches to ground anyway, the worst that happens is a spurious input.
This point of efficient design is precisely why input pull-ups are provided in the MCU and not pull-downs.
rm65453:
I thought they were just normal digital communication pins.
They are. But if you use the SPI at all, those are the pins you use, paralleled to the ICSP/ SPI header.