Primary slave drive would be the drive connected to the center connection on the primary ribbon cable - so yes it would be your second drive.
For backing up, you can either save the information to CD, DVD, or tape - depending on what you are set-up for.
My preferred method:
If you happen to have enough room on the Master drive (your first drive, which probably has the OS installed on it) - you can just copy the contents to the Master drive into say a folder called "Slave Backup" - then purchase a new drive > remove old drive > install new drive > format drive as a Logical drive (either a Primary, or as an Extended partition) > move the copied files onto the new drive.
Note - you can also use a combination of both CD/DVD, and copying data to Master drive - which would save some money in CD's/DVD's, and time due to faster transfer speeds to the Master drive.
This all assumes that your second (slave) drive does not have an operating system on it. If it does, you can use a program like Ghost, or DriveImage (which I believe Jafo uses) - then create a clone image of the old drive > swap drives > your done.
BTW - the only stupid question is the one you don't ask.