If the order you want to achieve can be defined using some of Calibre's metadata (e.g. Author/Series/Index/Title) then you can get your Collections to automatically resequence every time you connect using the special Sony tweak 'Specify how SONY collections are sorted'. If you also want to be able to 'see' this sequencing metadata the Metadata Plugboard will help.
An alternative option would be to use the send-to-device 'Save Template' to name the files appropriately so that when you sort your Collections by 'File Name' they come out in the right order.
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