There is an option that allows you to hide the inactive partitions that have the operating system installed on.
All it is doing is reassigning C to D or D to C, depending on which OS instance you decided to boot to.
So, if you get your startup menu:
1. Internet
2. Recording
If you pick option 1, than that partition is C: and the other OS partition is D:
If you pick option 2, than that partion becomes C: and the other OS partition becomes D:
As I said, there is a way of 'hiding' it, so that you will only see, C:, D:, and E:. I've havn't really found this to be of any great use though. Sometimes I'll be surfing the internet and download something to C:. Boot to my recording partition and want to grab that file from there. Sometimes I run out of space on my audio drive and move a song folder from there, to the inactive OS partition.
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After re-reading your post, I think you made a mistake when you installed your second OS, and your dual boot setup is not working correctly. Especially note step '7'.
Quick 12 steps with limited details:
1. Boot with the boot disk that has efdisk.exe, mrbooter.exe, format.com and CD-Drivers if needed.
2. Efdisk /mbr <enter> Setup your partition sizes, reboot with floppy and format both C and D. Format c: /s <enter>, then Format D: /s <enter>
3. Efdisk /mbr . Hide one partition 'H', make one bootable 'spacebar', F10, save, reboot without floppy.
4. You should only have a C drive now. From the A: prompt, type cd D: <enter> 'invalid drive specification' is what you should get. Install your cd rom drivers using the 'cd setup' thing.
5. Reboot. Test again, you should only have C: and E: (your cd-rom).
6. Install windows on c: Windows should give you the option of C: only if you hid the other partitition properly.
7: Reboot with bootdisk. Efdisk /mbr. Hide the partition you just installed windows on, make the other partition active 'spacebar' and unhidden 'h' (it probably already is not hidden), F10 save exit. Reboot without floppy.
8. You should once again, only have c: drive. Test this. Install your CD rom drivers using the CD Setup thing. Reboot without floppy.
9. You should have C and D (cd-rom). Test this. C should be blank as well. Your previous install of windows should not be accesable in any way.
10. Install Windows on this partition.
11. reboot with floppy, run mrbooter.exe, setup your boot menu names etc. save, exit, reboot without floppy.
12. should be working, hopefully.
I think where you may have mixed up is in the 'hiding' of partitions when doing the second install of windows.
Being able to 'see' both OS partitions is not a problem. But when you get that boot menu and boot to either operating system they should be 100% unique and isolated as far as programs installed, hardware profiles and registry etc.