There isn't much I can say about scanning since there are different firmwares and each of them is a little different.
All I can give you are tips.
1) Scan your manga at least at 400dpi or higher. Personally I use 600dpi.
2) Buy a simple cleaning product in your local supermarket. I use 'Glassex' (for the kitchen) myself.
3) Buy a cheap anti-dust cleaning cloth in your local supermarket, like Sorbo.
4) Clean your scannerbed regularly with these two products.
5) Bend your manga before you start scanning as much as possible.
6) Make sure you put your manga at least one centimeter away from the edge of your scanner. See example below:
7) If you're unsure that the manga will be scanned straight, search for a vertical line when you look below the scannerbed.
8) You can also use transparent tape. -->