Dual boot problem

I have a hard drive "C" which is about 1 GB and a second hard drive "D" which is about 1.6 GB.  I used Partition Magic 3.0 and created a 300 MB division on drive "C" called drive "E".  I then installed Windows 95 on the newly created drive "E".  The remainder of drive "C" has MS-DOS 6.22 along with Windows For Work Groups 3.11, which I always manually load from the DOS prompt if needed.  Next I installed System Commander 3.0 as my boot manager and I created three menu choices, 1) MS-DOS 6.22 - 2) Windows 95 - 3) Boot from drive "A".  Now here is my problem . . . When I pick option 1 I want my config.sys and autoexec.bat files to load . . . When I pick option 2 I don’t want my config.sys and autoexec.bat files to load.  Sounds easy, but I can’t figure it out for the life of me, please help!!
WGuerinAsked:
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umzilberCommented:
I have had the simular problem and here is how I solved it.  Partition Magic alows you to have two partitions active on one drive.  So if you have C and E active partitions you can install Windows 95 on E and have system commander recognize it as a bootable partition.  If you need more help.  write me direct

umzilber@mcs.drexel.edu
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