With photoshop all I have to do is set my pencil to 2 and make sure I dont click and drag.
for example im working on zinzolin overworld the number 2 pencil makes the exact size pixels I need. maybe its just all in my head but i just feel more comfortbale working with overworlds this way.
my battle background I scratch drew everything in 1 pixel then doubled the picture to what it will be in the game. and did any correcting from there with the 2 pixel pencil.
Even with anti aliasing on my photohop doesnt make the best transitions on the lines and curves even with the 1 pixel pencil so unless im scratch spriting or shading I draw in the size it will be in game by placing one pixel at a time.