Original texture size was 1024x1024 but I want to fit 2 textures in 1 image so I resized the texture to 512x512 in 1024x1024 image. Then I scaled UV Map to 0.5 and moved both x,y to 256,256 but it doesn’t align perfectly. What should I do?
seems like re-position issue. moving to (256,256) is not a precise operation
unless your original map is initially set exactly to the center of the image.
try using 2D cursor as pivot point when scaling. this will perform both scaling and
re-position via single action with proper handling of initial offsets.
You need to set it up like UDIMMs and then scale the UV’s to fit inside the single 0-1 UV range.
So you select your UV layout and move it a full step over (G, X, 1 in 2.8, or 'G, 'X, 1024 in 2.79 will move it one whole UV space from 0-1 to 1-2). Then do the same for Y. Then set your piviot to cursor and scale .5.
Then you bake from one UV map to the other with emission and render samples set to 1. No fiddly stuff to worry about that way. 
So the original textures will use the original UV map and you’ll bake a new texture using the new UV map. Emission bakes really fast, so no worries there.