Scope of stamp duty on shares: stamp duty: basics of a charge: principal instrument
If there are two or more documents which complete a sale, the principal instrument, that is the one which attracts the Stamp Duty (SD) charge, is determined by SA1891/S61. This effectively leaves the choice in the hands of the parties to the transaction.
This does not mean that SD can be avoided by splitting a transaction between two documents, executing and keeping one of them abroad and nominating that one as the principal document. In those circumstances the document to be used or recorded in the UK is liable to the full SD unless the other document is fully stamped. This follows from the judgement in Parinv (Hatfield) Ltd v IRC  STC 933;  STC 305(CA).
In Scotland, SA1891/S61(1)(c) states that any disposition or assignation by the seller is the principal document. If, however, there is no such disposition or assignation then it is up to the parties to decide which of the documents is the principal document and to pay SD accordingly.