I have chosen a multi-window design for my tool.
It will make for a less compact user interface - but it makes the code design easier, because each window can have its own isolated code function. This means that there is less chance of one section of code interfering with another.
In my design each window either executes code, or creates controls/sliders for attributes that have have been set up by the previous window.
The flow for the tool is like this:
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