I started AVR Studio 6.2 on my Windows machine. Clicked on File>>New>>Project, selected New Projec>>Assembler then selected the mega328P for the chip.

I went to this page: http://www.instructables.com/id/Command-Line-Assembly-Language-Programming-for-Ard-2/ and copied the code from step 3 into the editor into Studio. I commented out the two rcall delay lines in the blink loop.

I went to Menu: Build>>Build Solution. I got a "Build succeeded." message. Looking good!

I went to Menu: Debug>>Windows and selected I/O View. A window popped up. I clicked on the I/OPORTD selection to expand it. At the bottom of the window the contents of registers PIND, DDRD and PORTD are displayed.

I went to Menu: Debug and selected "Start debugging and break" The simulator jumped into the code window and the I pressed F11 (the step into key) and watched how the highlighted line increments. Take a look what happens to PORTD and PIND when you get into the blink loop.

Modify the code to do what you want from there. I think that should get you going.

EDIT: Just to make sure everything works I modified the code to blink all of PORTB so you can see how it's done.

Good Luck.

/*
 * AssemblerApplication2.asm
 *
 *  Created: 7/31/2015 6:25:07 AM
 *   Author: JMB
 */ 



.nolist
.include "./m328Pdef.inc"
.list

;==============
; Declarations:

.def temp = r16
.def overflows = r17


.org 0x0000              ; memory (PC) location of reset handler
rjmp Reset               ; jmp costs 2 cpu cycles and rjmp costs only 1
                         ; so unless you need to jump more than 8k bytes
                         ; you only need rjmp. Some microcontrollers therefore only 
                         ; have rjmp and not jmp
.org 0x0020              ; memory location of Timer0 overflow handler
rjmp overflow_handler    ; go here if a timer0 overflow interrupt occurs 

;============

Reset: 
   ldi temp,  0b00000101
   out TCCR0B, temp      ; set the Clock Selector Bits CS00, CS01, CS02 to 101
                         ; this puts Timer Counter0, TCNT0 in to FCPU/1024 mode
                         ; so it ticks at the CPU freq/1024
   ldi temp, 0b00000001
   sts TIMSK0, temp      ; set the Timer Overflow Interrupt Enable (TOIE0) bit 
                         ; of the Timer Interrupt Mask Register (TIMSK0)

   sei                   ; enable global interrupts -- equivalent to "sbi SREG, I"

   clr temp
   out TCNT0, temp       ; initialize the Timer/Counter to 0

   sbi DDRD, 4           ; set PD4 to output

   ldi temp,  0b11111111 ; going to set PORTB to outputs
   out DDRB, temp        ; it"s outputs
;======================
; Main body of program:

blink:
   ldi temp, 0b11111111
   out PORTB, temp
   sbi PORTD, 4          ; turn on LED on PD4
   ;rcall delay           ; delay will be 1/2 second
   ldi temp, 0b00000000
   out PORTB, temp
   cbi PORTD, 4          ; turn off LED on PD4
   ;rcall delay           ; delay will be 1/2 second
   rjmp blink            ; loop back to the start

delay:
   clr overflows         ; set overflows to 0 
   sec_count:
     cpi overflows,30    ; compare number of overflows and 30
   brne sec_count        ; branch to back to sec_count if not equal 
   ret                   ; if 30 overflows have occured return to blink

overflow_handler: 
   inc overflows         ; add 1 to the overflows variable
   cpi overflows, 61     ; compare with 61
   brne PC+2             ; Program Counter + 2 (skip next line) if not equal
   clr overflows         ; if 61 overflows occured reset the counter to zero
   reti                  ; return from interrupt