Oh, I see what you mean. You don’t want to scale the sprite in that case. You can’t scale 48x48 to 32x32 or 64x64 without some distortion of pixels.
What you want is to either pad or crop the sprites. If you look at the Configuration screen after the Customization screen, the top right has a section titled Padding. You can manipulate these values until the individual sprite size matches your desired sprite size.
Let me know if that makes sense.