<<I have two hard drives on my S900. The original 2Gb SCSI w/ OS8.6 and a
160Gb IDE w/ OS9.1. Am I asking for trouble by opening applications that are
stored on the SCSI drive when I'm running OS9.1 off the IDE as long as I
have any necessary control panels, extensions, etc. necessary to run the
program installed in my 9.1 system folder? >>

Not really, as long as you realize the the program will have preferences and 
application support files residing in both system folders.  If these have 
critical settings you may want to insure they are synchronized.  You can usually 
just drag copy them from one system folder to the appropriate location in the 
other.  

<<Am I not realizing the full
benefit of the faster IDE drive by running an application that is istalled
on the SCSI?>>

It depends on how frequently the program accesses the hard disk to read or 
write support and data files.  The difference in speed may be hardly noticeable. 
 Or if a scratch disk is involved it could be significant.  In this case make 
sure the IDE disk is designated for scratch, preferably a dedicated partition 
if scratch use is heavy.

<<Should I re-install all the programs that are compatible w/ OS9.1 on the 
IDE?>>

Your choice.  There is no compelling reason to separate OS8.6 use and OS9.1 
use physically, other than keeping the system folders on separate volumes as 
you do.  However, these separate volumes could reside on the same hard disk (the 
IDE).  With the large capacity of new IDE drives the small stock SCSI drives 
might be considered dispensable and some people use all-IDE configurations.  I 
use a small SCSI HDD for online backup of the system and applications.

-Bruce Holifield

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