The .tar.md5 files are .tar files with the md5 checksum added to the end of the file. If you attempt to flash a .tar.md5 file, Odin will automatically check that the contents are what they should be before flashing and proceed with the flash if the md5 is valid, otherwise it will stop.
In Odin, you should use the PDA button for all flashing. The PIT button may be used as well, if we can get a valid .pit file for the device, but for now, PIT won't be used either. Other than PDA, Start/Reset are the only other buttons you need to worry about.
Now, on to creating the backup files. First, you will need your device to be rooted (perm or temp root will work), and you also need to have access to terminal on the phone, either via an emulator or adb shell access. To create the backup files, you won't need a Linux/UNIX system, but you will if you want to create a flashable Odin package. The following will output the files on the root of the SDCard, adjust the "of=" path if you want them somewhere else. It will also create the files for the proper filename for Odin as well. So to create the files, here are the commands you will use from root shell (#):
dd if=/dev/block/stl10 of=/sdcard/factoryfs.rfs bs=4096
dd if=/dev/block/bml8 of=/sdcard/zImage bs=4096
dd if=/dev/block/bml9 of=/sdcard/recovery.bin bs=4096
dd if=/dev/block/mmcblk0p3 of=/sdcard/cache.rfs bs=4096
dd if=/dev/block/stl11 of=/sdcard/dbdata.rfs bs=4096
dd if=/dev/block/mmcblk0p1 of=/sdcard/movinand.bin bs=4096
To create a flashable Odin package, you need to pull all of the files off of the phone/sdcard and onto your computer. From there, you use the following to create the package:
tar -H ustar -c factoryfs.rfs recovery.bin zImage > package_name.tar md5sum -t package_name.tar >> package_name.tar mv package_name.tar package_name.tar.md5
There are other files that may be in Odin packages, but they are protected by Samsung and cannot be dumped properly. The files are the bootloader, secondary bootloader, modems, and .lfs partitions. The files would be boot.bin, Sbl.bin, modem.bin (not sure what it would be for the CDMA/LTE dual modem here), and param.lfs. It however isn't that big of an issue that these can't be dumped as the can't really be altered by normal flashing of the device, and are usually only altered via OTA updates.