Yeah, the recovery console can do it for you. The automatic recovery stuff will try to find your Windows partition (I believe it looks for some specific files, like c:\windows\blahblah.dll, but that's just my theory) but it doesn't always succeed. If you're comfortable using the manual tools you should be able to recover from pretty much anything so long as you have all the files in place. You need a boot sector (fixboot can do this), a boot loader, and for NTLDR you need a boot.ini pointing to the correct Windows partition and directory (this is where Recovery console sometimes chokes).
The only time it gets tricky is if the order of your drives changes for some reason. I can't remember the exact syntax of boot.ini off the top of my head (on a Mac right now) but it's got a line something like
disk(0)partition(1)blah(0)=c:\windows that tells NTLDR exactly where to find the Windows directory. All you have to do is figure out which "disk" or "rdisk" and all the other variables are correct for your boot partition and you're all set. You can even make a ton of lines in boot.ini with every possible combination and just tick through them all. I did that once when I ran out of patience on a crazy test server we had that had multiple SCSI and IDE controllers.

That said, if you're A) only backing up every couple months, and B) don't care about losing data from the interim period, and C) want to be able to restore a system fully with no hassles, I would just bring the machine down, boot to a USB hard drive with imaging software on it, and push the image to that hard drive. When you want to restore, just boot to the USB hard drive, restore the image, and you're off to the races. It really is the easiest way to back up and restore a FULL system. It's awful for traditional backups where you want to restore a few files and back up a running system, but your needs seem to be a special case to me.
Doing imaging you don't need to mess around with the registry, worry about which files are in use and were not backed up, or screw around with MBRs and boot loaders. All you have to do is point the software at the right drive and wait. Like I said before Symantec Ghost 11 is what I use at work, but it's not free. Clonezilla is an open source alternative but is harder to use. I would be you could even use Carbon Copy Cloner on a Mac if you have access to one, as that's shareware.
If you do go with a traditional file backup, everything in Windows (except the boot stuff) is just files, so when you back up all the files you've backed up the whole computer, settings and all. (The only exception to this is a few REALLY naughty apps that write crap into your drive headers for copy protection purposes. Adobe is the only one that I know still likes to do this.)
Either way,
test your restore! I don't mean to sound rude, but the worst feeling in the world is realizing the backup you've been doing for years is worthless the first time you need it. Just grab a spare hard drive and do a restore to it, then try to get it booting like your original drive. All these questions will be quickly answered when you work through using the recovery console or imaging software, whichever path you choose. You'll feel a lot better knowing you have a backup AND you know exactly how to make it work
before the whole machine melts down.
(FWIW, for my backups I've just walked away from backing up Windows and only back up the arcade files. This works for me because I don't mind spending an hour letting XP install itself and another couple hours installing apps like video codecs and Windows Updates... at least for my home arcade I don't.)