Issues with linked files, should I RAID?

So, my first Mac (which was a hand me down) had the two drives RAIDed. But when I was ordering my new mac the guys at mac seemed opposed to the notion of doing this. Now I find that I have difficulty working in some programs, like Adobe InDesign. The program can't find links on the second drive. The tech support at mac suggested RAIDing the drives might be a solution, but only as a last resort (they told me to call Adobe). When I talked with Adobe they said it was a Mac issue, since I was having similar difficulties with other software (non-Mac, non-adobe). So is this a format issue? I mean did I miss a step and my second drive isn't formated properly? Has anyone else had this sort of issue (or do you know anything about this issue)? Both Mac and Adobe told me they hadn't heard of this issue before. I can't imagine I am alone in the world on this one. But I am willing to accept that I have done something wrong (or not done something) to incur the wrath of my software. Thanks for any advisement.

No I have not checked for where my scratch volume is located. I don't know how. I am not entirely certain what that means.
I do work with large files, just about everything I do is in an Adobe program. Performance (as far as speed, I have 8GB RAM) is not an issue.
When you say "seems like it wasn't installed properly" do you mean when the guys put it together they didn't get it in right/ damaged in shipping, or do mean when I set up applications, preferences, etc. I made some error? I only have 2 drives, 350GB, and 750 GB. When I was building (I mean telling the Mac guy what I thought I wanted and asking his recommendations) this machine he told me that Adobe software has trouble utilizing more than 2 Drives.
So perhaps the ownership is wrong, but I don't really know how to work toward change on this issue. If you have any suggestions I would really appreciate it.

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