Just to be sure it is this you have been rreading?
http://www.arduino.cc/en/Reference/PortManipulation
So:-
How do i read the inputs from say PORTB?
int input_value;
input_value = PORTB;
This returns 8 bits but only 6 are meaningful for this port.
lets say PORTB reads '110011' what will the value stored in input_value?
It is simply the binary value 110011, all numbers are binary, if you get it to print this as hex it will read 33, in decimal it will be 51 but it will still be 110011 inside the Arduino.
finally what will read on the analog PORTC return
The logic value of the bits on each pin, if you are putting analogue values on it then it depends if these values are above or below the logic threshold.
how do i get the corresponding analog values
By using analogRead(), or by selecting the appropriate multiplex input, initiating a conversion and reading the results register when it is finished, all by banging bits in other resisters. (but why bother)