you can do it through code:
as an example:
SPList list = web.Lists["My List"];
list.EnableVersioning = true;
so the above can be simply added to your code when your creating the list:
somthing on the lines of:
//get web object from context
SPWeb web = SPContext.Current.Web;
//get list collection
SPListCollection lists = Web.Lists;
//add list to list collection
lists.Add("My List", "My list for user input form", SPListTemplateType.GenericList);
//call list that we just made
SPList newMyList = Web.Lists["My List"];
//enable versioning on that list
newMyList.EnableVersioning = true;
http://msdn.microsoft.com/en-us/library/microsoft.sharepoint.splist.enableversioning.aspx