Hey Al, - I like to leave the lid up when scanning. I think it gives better contrast (you can also adjust this after the fact). It also doesn't leave those white corners where you see the gasket edges in your scans.
If you're using the supplied software, click "Scanner Driver" then Preview to scan the whole glass, then select the area you want to scan and press scan.
You can also adjust the dpi that it scans. If you want more detail, go with a higher number but also know that it will be a larger file size. I do bulk scanning at 300 dpi but if I want clarity in faces of a postcard or something to zoom in on, I go 800 dpi.
Feel free to pm me if you have more specific questions or want more tips.
