Before you to scan, you need to prepare the manga.
First you have to decide if your going to cut/debind the manga.
If you decide not to cut your manga, then the other choice is to get lower quality scans, or to press VERY hard.
I recommend you cut/debind you manga if your willing to sacrifice.
Before you begin to scan, you need to know how to get the scans. I presume you have the scanner installed and it's working.
There are several programs that you can use for scanning, and as long as they are "twain compliant" they should work. Usual place it is located is, File->Acquire or File->Import
You might also need to state which hardware to use by going into the settings.
The problem with scanning, is that many people have different programs depending what scanner they have, but here's an example with Visioneer Scan Manager Pro. I recommend you try and line the pages along the edge to get a straight scan if possible.
FOR COLOR SCANS, MAKE SURE YOU SCAN IN "COLOR" or "RGB" MODE.
You should also try to play around with the scan area, and save the settings if possible. That way you don't have to scan the whole thing, and instead just scan the area with the cover/pic.
Recommended settings for color is 600dpi, and save in jpg format around level 7 to 8 or 70 to 80, and in a color or rgb setting.
What to do with color images:
After you scan a color image, you might want to play around with the curves in PhotoShop to get a better picture.
Black and white scans are what you are probably going to spend most of your time scanning, example.
FOR BLACK & WHITE SCANS, MAKE SURE YOU SCAN IN "GRAYSCALE" MODE.
If you are placing the picture along the edge, you can set it so that the scanner only scan's around that area. I use a setting of around 4.3" x 6.8" (as seen in the example) and the resulting scan is automatically cropped. The final result is this (unchanged except for resized).
Recommended settings for black and white scans are 300dpi, and save in jpg format, around level 7 to 8 or 70 to 80, and in grayscale mode.
You can also play around with the brightness and contrast if you want. Check which settings you like. I use a low setting, no more then 10.
Cropping the file: If you want, you can crop the file. This is done by making a marquee and selecting in PhotoShop, Image->Crop. This is fairly simple and you should be able to do it yourself, however it is usually done by the editor.
Tilt the pic: Tilt is something else you could do, but this is also usually done by the editor.
I personally use irfan-view for scanning. Not only is it free, but it has a batch scanning feature which i used to rename the file.
First got to File->Batch Scanning
It'll look like this.
Put output file as the name of the file and string index as the page number or whatever, and the directory as the output directory. Also select in options and make sure it's set tp save as Grayscale.
Scan as you would a normal black and white picture. IrfanView will automatically save the file for you after you scan it. Then repeat for the next picture, only increment the Index number accordingly. This saves in the time that it takes to rename the files, and you wont forget to save the file, cause it automatically does it for you ^^.
Well that's basically it. It's up to you to actually use this information and apply it to the scans and if you have any questions: DON'T BUG ME FOR THE ANSWER =P.