Comparison is done in real time, so you do not have to prepare for it in any way (short of having snapshots to compare with in the first place of course). It simply works by taking two sources, typically what is in the editor and what you have selected in the snapshot pane, and right then and there comparing the differences between the two, using the level of granularity selected for comparison in the dropdown arrow button alongside the Compare button.
As soon as you do anything to leave that view, the comparison is discarded, it only ever “exists” while you are looking at it—and can thus be better thought of as a way of viewing a snapshot.
As noted, Import as a feature creates a whole new item in the binder, unbound to any existing items and thus any of their snapshot lists. So to basically “import” the history of a file you would want to use copy and paste. Import would work fine for the initial phase of course.
Here are a few other tips:
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You can compare snapshots themselves rather than simply comparing the selected snapshot with the current text. This way you can get a view of what has changed between the original FileMaker source and the later AppleWorks source, even if there is a newer FileMaker snapshot, or an even newer Scrivener edit in the main editor. To do so, simply Cmd-click to select multiple snapshots in the pane, then click Compare.
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Comparison doesn’t have to be done in the inspector; it’s convenient, but sometimes making use of the split editor feature is a better interface for reviewing many changes. To do that, hold down Option and drag the snapshot to a split editor’s header bar (if you don’t hold down Option it just loads the snapshot in the editor normally). Note the Documents/Snapshots/Show Changes/ submenu contains keyboard shortcuts for jumping between changes—something you might find handy since the editor won’t have those next/prev buttons.
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If you do want to preserve the comparison for whatever reason, you can do so. The text comparison view is comprised of formatting that you can copy and paste anywhere, such as the Notes panel for that document or even a new item in the binder entirely. This might be handy if you are working with a comparison extensively, and find having to recreate the comparison session over and over a bit awkward.
You can combine the above trick with this one by selecting two snapshots in the list and Option-dragging them to a header bar.