since I backed my 10.4.11 system onto my external HD, do I need the physical disks for 10.3.9 in order to upgrade to 10.4 and so on onto the partition?
No. You may use a cloning utility such a SuperDuper.
Can I just drag the folder that has 10.4.11 in it from my external HD to the partition as is, in toto?
No. Use the cloning utility. In this way, the hidden files, the unnecessary files and the proper links and such will all be taken care of to creat an identical, bootable volume.
Does this take a bunch of time?
The initial creation (duplication) varies on the size of the volume being cloned. From 15 minutes to an hour is common.
assuming I'm going to partition, do I need to set up a separate password, etc, to get to the new partitioned area I want for scanning?
If you clone, when you boot to the new partition, you will use the same password.
Even if you install new, you may set the same password.
then I would need to make it my startup preference, right?
Either that, or, hold Option (Alt on Windows keyboards) when you start up. This brings up the Startup Manager and allows you to choose which volume to boot to.
Also, is the folder that contains the backup of my old system enough as reference 10.4?
As long as the backup is bootable, you may clone it to another drive or even just boot to it.
Or do I need a physical installation disk for 10.4 or 10.3? Can the OS be updated just the same as my tower?
Consider each new hard drive or each new partition as another "computer". The thing is, all these reside within the same machine.
So, which each new drive or volume, you install and set up your OS as you did when you first bought and setup your computer.
All these new systems can reside in one machine. You may boot between them at will, but cannot run two (or more) at the same time.
If you use clone utilities such as SuperDuper, then you only need to install an OS and applications once.
After that, using the clone utility, you can recreate a duplicate at anytime, and use the utility to keep an identical backup, to which you may also boot.
Use the Startup manager to choose which you wish to boot to, and leave the Startup drive preference in the system preferences set to the drive/volume that you use the most.