New to Acrobat Pro 9 - Issues with Portfolio Management

All
With apologies, I am completely new to Acrobat Pro 9 - and this may have been answered before.
I am using Acrobat Pro 9 as, hopefully, a file management system (in a Mac environment).  I want to be able to take all of my files - native format - and combine them into one portflio and arrange them in a certain order.
No problem in creating the portfolio and dropping in the files, but I can't get them to arrange in the order I want.  When someone opens the file, I want them to be able to see the file layered as if it were a paper file.  So, for example, the most recent email would be on top, with the attachments going with that email directly behind it, then the previous correspondence behind that, a presentation given behind that, etc.
The problem I have is that when I deposit the documents in the file, they are randomly assembled.  I don't want to use the sort chronologically button as the date created does not always reflect the actual date of the correspondence.
Also, I am hoping that I can later add documents to the file not only on top (the most recent) but in the middle if I find a missing document, for example.
I have tried creating a new tab to order the documents, but as soon as I start numbering them in order, the numbering of the others gets revised.  Very frustrating (plus with this method you would constantly have to renumber all the files everytime you added a new one).
Please tell me this is possible and, if so, what I need to do.  I am assuming it is a simple thing, so thank you in advance for any assistance you may be able to offer.

Thank you for your response.  I got an error message as follows:
%%[ ProductName: Distiller ]%%
%%[ Error: undefined; OffendingCommand: MSPUB_setclippath_7 ]%%
Stack:
[0.0 -1.0 1.0 0.0 -10200.0 6600.5]
%%[ Flushing: rest of job (to end-of-file) will be ignored ]%%
%%[ Warning: PostScript error. No PDF file produced. ] %%
Any ideas?

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