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I think this is a classic case of distinguishing between how the software
presents choices and how the user views their choices.
>From the user perspective, they probably either want to create a new query
or temporarily change an existing query. It is only once they make this
decision that they think about *how* they might best create their new query.
(Of course you'll need to check this with your own users.)
I would look into combining the "create from scratch" and "create from
existing" options into one topic--equal to "modifying existing", which, as
you say, is the most common task.
Since I don't know the software, I can't get very specific. But remember
that even if the software seems to present the user with three choices (such
as three buttons in a dialog box), that doesn't mean you have to model your
instructions that way.
Example:
_______________________________
Creating a New Query
Blah blah blah creating a new query...
When designing a new query, you have the option of using an existing query
as a base.
(See--here you are talking about creating a new query, and presenting the
"modify" feature as an alternative option to the standard "create"
procedure. Depending on how the software works, you can either integrate
the scratch/modify options into a single list of instructions, or you can
present the "create" instructions, followed by the alternative "modify"
instructions, without using the scratch term.)