First, separate the scanning process from the post processing process. Do this by scanning as a picture at a higher resolution 300-600DPI or more. The files will be large, but only temporary until you post process. File size will be your biggest slow down here, so drop your resolution and bit depth to as low as comfortably possible. (e.g. use grey scale if you do not need color). What you do not want are 24bit 1200DPI image at 8-1/2"x11" that are 100's of MB's each unless you have to; they take too long to save and open.
Then using any software that suits your needs, run your post processing in a batch at your convenience. All software functions differently, so you will have to learn your software.
Here is the catch though. Most programs only run on 1 core of your multi-core CPU, so the best way to make things run faster is to open your program multiple times and split the batches between the open instances of the program. Most programs will not open multiple instances, so you have to run the program from either the start menu manually, or from the run command with a special "switch". Depending on your program depends on how you do it. Acrobat for example needs to be ran from the run command as "ACROBAT /N" to open a new instance if an instance is already open.
If I have upwards of 10,000 pages to post process, then during the day I will open 3 instances on a 4 core computer and split up the jobs across the 3 instances so I can still use the computer (the CPU runs at 75% leaving 25% for "office use"). At night, I will run 4 instances to max out the computer.
But if I know the post processing will not take that long, say only a few hours, I won't bother with opening up instances; I will simply run a batch and let it go until is complete. With a dual core computer, this would allow you do run your post processing and still use the computer. Most batches will not take that long. be aware if you run 2-3 instances on dual core computer, your computer may not function as a desktop for active use until the batches finish.
Another option, no matter if you run instances or not, is to go into the windows task manager and change the CPU priority for the instances to below-normal so your active work takes precedence over the background post processing.
As for the speed, the more cores working, the faster processing will go. The problem is if you have a dual core CPU that you run a single threaded app on, and you buy a comparable quad core and run the same app in the same manner, it will not go any faster. So, the trick is to run your single threaded app multiple times at the same time to max out you CPU's capabilities.
At the end of the post processing, save the document(s) in your desired format, then QC batch before deleting the images.
If you use Acrobat and you run large batches, be ready for problems though! Search for solutions and find more people with the same problems too! Acrobat is a PAIN!