These are all very good questions and I will try to shed some light on them for you.
The Linux file system is a flat file system with everything under / which is also known as root. In Windows, each partition, or logical drive, has a drive letter assigned to it such as C:, D:. This is not the case in Linux; it is all flat under the one structure. You have been doing some reading, which is great and I would recommend that you try to find some documentation on the layout of the file system. It does follow an organized pattern and once you "get it" it will make sense, though it will probably take a while till this just happens. Here is a great resource for you: http://ftacademy.org/materials/fsm/13
(the other resources on that site are good too but start with that).
Here is a short description of the major partitions:
/ Root, is the root of the file system, the base of the tree
/bin, /sbin contain binary application files, related to the system (sbin) and other functions (mostly utilities) /bin
/usr and /usr/bin, /usr/sbin, and the like under /usr are reserved for the user to install binary application files
/etc contains application configuration files. This will be one of the primary directories you learn to work in
/home contains all the home directories of the various users
/var contains information that will change often, such as log files
/dev and /proc are pseudo file systems. Everything in Linux is treated as a file, including the USB sticks, mouse, keyboard, etc. And these directories are associated with the hardware. Consequently, your drive partitions will appear under the /dev for device "files". /dev/sda1 is the first partition on the first drive, /dev/sda2 is the second and so forth. Similarly, /dev/sdb1 and /dev/sdb2 will be the first and second partition on the second hard drive.
My recommendation would be to create the following: / and make it moderately sized. 20-50 GB should be sufficient. /home make fairly large. You can have multiple users in the /home space and if you install multiple distributions, each will need a separate / partition, but you can share /home (just use different users and you will have no conflicts). I would also create some swap space. Back in the old days of little memory, 1-2x you phyiscal memory was good. These days it is a waste. I would recommend 1-2 GB of swap space as more than sufficient. Unless you start running a lot of applications or virtual machines you probably won't be wanting for physical memory.
Your / /home, etc can be what ever file system you would like. Generally speaking, Linux users go with the EXT (or extended file system) with EXT4 being the latest incarnation. EXT is what is called a journaling file system which isn't subject to fragmentation like FAT or NTFS. If you want to share between Windows and Linux, you can use a USB Stick or a SAMBA server or whatever. I wouldn't worry too much about creating a FAT or NTFS partition just to share stuff between. Linux can read the NTFS and you can always work from there to move between the hard drives.
The above partitions would be on your new drive (for Linux). Create the three partitions and install Linux after Windows. This is called Dual Booting. It will put a new boot loader on your primary drive and partition (with Windows) and let you select between the operating systems. If/When you decide you want to remove Windows, you can remove the drive and update your boot loader to point to your remaining drive. Linux is very forgiving and adaptable about hardware changes.
Lastly, with IDE and SATA drives you can have some many (4) primary partitions. Beyond this you need extended partitions, where your last primary partition becomes a shell that holds all the other Logical partitions. Nothing really too it, it is just a way to get more than 4 partitions on a drive.
Hope that helps, but if not, ask away.