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How do I create a form such that the document set is returned when the form is submitted?

First get a hold of the corresponding FormTypeEntry and then specify the _formActionDocs parameter as true when creating the FormEntry.

FormTypeEntry formTypeEntry = ...; // find the correct formtype entry

// request all data come back as part of the submit response 
NameValueCollection linkParams = new NameValueCollection();
linkParams.Add("_formActionDocs", "true");  
linkParams.Add("_data","{FirstName:TestA,LastName:TestB}");

FormEntry formEntry = formTypeEntry.CreateFormEntry(linkParams);

How do I pre-populate values when creating an instance?

When creating a form instance, you can supply data to pre-populate fields.  There are a couple of ways to do this.  The first way is to supply a name value collection, which holds control names and values.  The second way is to supply an XML document, with control names and values. Suppose your form has two text fields, named A and B respectively.  Also, suppose you wish to prefill these 2 controls with values, as shown:

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