Time Machine Backup: separate configurations for different drives?
&quot;A few times a year I back up pretty much everything to that.&quot;
I suggest you use a cloning software package for making your once in awhile copies.
I use Time Machine to get a historic copies of my files and a cloning software package to get a bootable clone of my Startup Disk.
Carbon Copy Cloner will copy your Startup Disk to an external  FireWire drive.  You can boot from the external drive to verify that you have a good clone. When you upgrade your existing Startup Disk, you can at any time boot from your external drive and go back to your existing system.
Slightly modified excerpts from SuperDuper's webpage...

SuperDuper is the wildly acclaimed program that makes recovery
painless, because it makes creating a fully bootable backup painless.
It's incredibly clear, friendly interface is understandable, easy to
use, and SuperDuper's built-in scheduler makes it trivial to back up
automatically. And it runs beautifully on both Intel and PowerPC Macs!
Give SuperDuper a workout on your own system. Clone to your heart's
content, for free. See what else is possible. When you're convinced
that SuperDuper is a terrific solution — and a great value at $27.95 —
you can register right from the application and start using its
advanced features immediately!

Disk Utility
Apple has included an option in Disk Utility – ‘Restore’. This option in Disk Utility allows you to copy the entire data of your hard disk to another hard drive or any external media.
dd command
-- the dd command is not for amateurs. -- you have been warned. --
You can use the dd command to backup a drive or partition. You need to be familiar with /Applications/Utilities/Terminal.  I added this section for completeness.
# save
dd if=/dev/disk0s10 bs=4096m | gzip | dd of=~/disk0-s10 bs=4096m
# restore
dd if=~/disk0-s10 bs=4096m | gunzip | dd of=/dev/disk0s10 bs=4096m


This is riskie if you have never done it before. It may be hard to figure out the correct drive name.

How do use dd:
get a second disk the same size or larger.

What the unix name of the disk will be depends on how you attach the disk. 

without the old drive attached to
diskutil list
df


attach the new drive before booting.
repeat the above so you can figure out the name.

Now, that you name the names, you can copy the old disk, /dev/disk0,  to the new disk, /dev/disk1.  

sudo dd if=/dev/disk0 bs=4096m |  sudo dd of=/dev/disk1 bs=4096m

# this command should do a block by block copy
# this way you will get the whole disk.
# if= is input
# of= is output

mac $ diskutil list
/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *1.0 TB     disk0
   1:                        EFI EFI                     209.7 MB   disk0s1
   2:          Apple_CoreStorage                         999.3 GB   disk0s2
   3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3
/dev/disk1
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                  Apple_HFS Macintosh HD           *999.0 GB   disk1
                                 Logical Volume on disk0s2
                                 B5476F09-70EA-41C6-8655-72485151AD19
                                 Unencrypted
/dev/disk2
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *4.0 TB     disk2
   1:                        EFI EFI                     209.7 MB   disk2s1
   2:                  Apple_HFS Backup - Mac Mini       999.3 GB   disk2s2
   3:                 Apple_Boot Recovery HD             784.2 MB   disk2s3
   4:                  Apple_HFS Backup - Time Machine   2.0 TB     disk2s4
   5:                  Apple_HFS Boot - for Fun          49.5 GB    disk2s5
   6:                 Apple_Boot Recovery HD             650.0 MB   disk2s6
   7:                  Apple_HFS 1T Backup               985.1 GB   disk2s7
mac $ 
mac $ df
Filesystem      Size   Used  Avail Capacity   iused    ifree %iused  Mounted on
/dev/disk1     930Gi  864Gi   66Gi    93% 226596185 17296037   93%   /
devfs          193Ki  193Ki    0Bi   100%       669        0  100%   /dev
map -hosts       0Bi    0Bi    0Bi   100%         0        0  100%   /net
map auto_home    0Bi    0Bi    0Bi   100%         0        0  100%   /home
/dev/disk2s2   931Gi  765Gi  166Gi    83% 200428475 43553456   82%   /Volumes/Backup - Mac Mini
/dev/disk2s4   1.8Ti  1.6Ti  147Gi    92% 441119165 38598628   92%   /Volumes/Backup - Time Machine
/dev/disk2s5    46Gi   29Gi   17Gi    63%   7590207  4490899   63%   /Volumes/Boot - for Fun
/dev/disk2s7   917Gi  771Gi  147Gi    84% 202019436 38487474   84%   /Volumes/1T Backup
mac $ 

http://www.stellarclonedrive.com/disk-utility-to-clone-mac-drive.php