For problem one… you could write a script to put all the docs in one dir. you could then run the script when ever you want using cron. and then use yast to backup your directory .the plan is not fool proofe and i could give you several reasons i would rather change my use of directorys and have all the backupd files in one directory and work from that one.
for the second question maybe some one else can hel you, because i cant.
YaST backup is intended for the system. For anything in your /home folder, just use K3b to copy them to CD or DVD - or back the files up on a USB stick.
Most USB sticks come formatted for Windows (vfat in Linux speak) and, though it is possible to reformat them to Ext2 in order to use Linux permissions, you need to know whether that will create other problems for you.
For problem 2: To protect folders on your USB: you can zip or rar the folder and add a password to them. Not sure if it works the same way in Windows and in Linux, that is if you encrypt in Windows, will the correct password unlock also in Linux? This i do not know. But rar and zip format both give the option of adding a password