AVR-ATmega256 What is the use of PORTxn?
Driven High - The signal is driven to your positive voltage (VCC)

Driven Low  - The signal is driven down to ground (GND)

Pull-up resistor:
In short, this means that there is an internal resistor that is connecting the pin to your positive voltage, thus driving it high unless a connection to GND happens.  Sparkfun has an amazing tutorial

Should your PORT register have a mix of pins defined as inputs and outputs, you can still read the values just fine.  To read the pins defined as inputs, you'd read the PIN register like so:
uint8_t inputs = PINx;

As for the outputs though, you can just set the PORTx register and you won't have to worry about it affecting the inputs:
Say you have pin 2 defined as an input and the others as outputs, writing a value like this, PORTx = 0b10001111 , won't affect the value for the input pin and will set all the others to the respective values.  Arduino has a good article on this