How can I make my scans look perfect?
I admit that I scan my artwork first then perform all my repairs using Photoshop Elements, ignoring the accompanying scanner software. It's just sometimes easier and faster to do everything in one application. This is doubly true when using specialist tools that are not part of the scanning suite, like the Burn and Dodge Brush Tools and even the Shadows/Highlights tool (Enhance > Adjust Lighting > Shadows/Highlights). Use these to darken or lighten shadow, highlights, or the important mid-tone contrast.
If the scanned file contains uneven tones—and many do due to poor storage conditions, fading, and chemical staining—use the Burn and Dodge Brush Tools (Tool Bar > Burn/Dodge) to 'paint in' darkness or lightness where required. Fine-tune the tool via its Options Panel. Go slow: always set the speed of the tool (called Exposure) to a low value to avoid leaving tell-tale retouching marks.