Why are my system and boot partitions now on seperate drives?

[willspringer]

Ok, I have four hard drives, only one of which I partitioned during initial Windows installation. It is a 250gb HD and I seperated it into 80 gigs and (almost) 170 gigs. The small partition was for Windows XP and programs while the larger partition was for games.
My problem started when I decided to reformat and repartition. I wanted a 35 gig partition just for Windows. I plan to use the other partition for all other programs (photoshop, media players, games, etc).
After the reformat, Disk Management shows that the new 35 gig partition is my system drive, and another 250 gig drive that I didn't think I had changed is my boot drive.
Why aren't the boot part and the system part on the same partition? In the past I believe I only saw a system partition (I assume the boot part was lumped in with it). How can I get the boot partition on the same partition as Windows? Can I just copy the boot files (autoexec.bat, ntldr) from the wrong drive to the correct drive?
My goal is to keep 3 drives with media only, no system files. Now one of them is a "boot" drive according to Windows Disk Management. I'm going crazy...

 

[Tmagic650]

What are your complete system specs?

 

[IronDuke]

You'll need to edit boot.ini to point to the revised partition.

Link

 

[willspringer]

update

My problem is (mostly) solved. I couldn't simply copy the boot files to the correct drive. What I did was take my main hard drive (the partitioned one with Windows) and stick it in another computer to reformat it. Then I put it back in my computer and unplugged all of my other hard drives. I booted off of my XP disk and did a fresh install of Windows (properly partitioned the way I wanted, of course). After setting up and updating Windows I plugged the 3 other hard drives in. I had to mess with the order the drives booted in in the BIOS before Windows would start again, but it all ended up working out.
The only problem is that the 250 gig drive that became my boot drive (the one I didn't mess with during my first Windows reinstall) is now marked as "active". My simple understanding is that this means it is almost a back up hard drive for my computers boot process (I'm not sure if that's true). This "active" partition rings a bell, I think a long time ago I accidentally marked this drive as active through disk management.

I'm not exactly sure what specs to post but I think these are the pertinent ones:
Gigabyte nForce4 SLI motherboard
AMD Athlon 64 3800+ Socket 939
4 gigs dual channel RAM DDR400 PC-3200 (clock 3-4-4-8)
Win XP SP2
nvidea geForce 7600 GS (cheap brand, I think Chaintech)

The 4 hard drives are:
Maxtor 250GB (now in 2 partitions, 34GB part. is system)
Western Digital 250GB (now 'active')
Western Digital 320GB
Western Digital 500GB
All SATA2 and (I believe) 7200RPM

I plan to either back up and reformat the 'active' drive, or just let it be, I'm not sure yet.

 

[IronDuke]

The partition needs to be set to 'active' to be bootable.

 

[rf6647]

Long on questions, short on answers

The quick answer - I believe everything is normal.
Disk Management would show 35gb part on Disk 0 as System.
Disk Management would show Disk 1, 250gb, Active. This tracks with an observation earlier in this thread that it was designated 'boot'.

If you question which drive is the current operating system, a simple experiment involves unplugging extra drives. Make a visible change to your desktop (change background; add extra shortcut ). Unplug extra drives. Restart computer. If the observed desktop matches the change, this confirms the disk used. You most recent post, to my way of thinking, already confirms this is true.

If your real question is trying to determine if disk 1 is bootable, change boot.ini to make disk 1 a menu choice. The discussion thus far did not relate any previous history that disk 1 ever worked as a boot device. Of course, this drive could be a legacy from ages ago (win98, etc.).

I must re-think the last sentence - I assumed the re-partition was performed in another computer. Now I am not certain, and hence, I have arrived back at the beginning and my long list of questions. I am interested in this discussion trying to understand which changes to drives corrupt the boot sector code and how to pick the action that avoids it or restores it.

My apology if this adds noise to the discussion.