I have a similar situation and I do a combination of conditional text and 
separate books. When I make the final PDF copies, I change out the title 
page for each separate book, show the correct conditional text, update the 
book, and create the PDF for the customers.
In my case, most of the text is the same in the chapters, so the conditions 
I address with changes are generally the same ones. This does make it easier 
to update changes to the software, and I usually have my chapters set to 
show all the conditions, so that when I search for the specific areas of 
text to update, I'll find them all in the first pass...

> ------------------------------
> Message: 59
> Date: Thu, 18 Oct 2007 15:43:38 -0700 (PDT)
> From: Sw D <swd12422 at yahoo.com>
> Subject: How would you organize these documents?
> To: Framers at lists.frameusers.com
> Message-ID: <153366.92561.qm at web44906.mail.sp1.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
> Hi, everyone-
> I am using unstructured FM 7.2 (Windows) to maintain the documentation set 
> for a suite of software products. We have several different customers who 
> each receive a different subset of modules, depending on their business 
> needs. Each module can be customized for each client, so that a client 
> that gets Module A might receive different functionality than another 
> client.
> In short, each customer receives its "own" version of the software. IOW, 
> Customer 1 gets Software Suite v. 5.6 that includes Module A, C, and E. 
> Customer 2 gets Software Suite v. 5.7 that includes Module A, B, and D. 
> BUT the Module A that Customer 1 gets might be different than the Module A 
> that Customer 2 gets.
> I started out documenting the "out of the box" settings in the user 
> guides, and then thought I'd just put the differences for each customer 
> into customized Release Notes. However, new customers don't receive any 
> release notes, and isn't it incorrect to send a customer a book describing 
> the functionality and features of Module A when they might not be able to 
> see/use everything documented therein?
> How would you maintain these files? Conditional text? Separate books? I'm 
> not sure where to begin here.
> Thanks in advance
> __________________________________________________

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