The following worked for me in the end. Answered in case anyone finds this thread with a similar problem in future.
private void openPdfInPolarisOffice(File myPdfFile) {
Intent i = new Intent(Intent.ACTION_VIEW);
i.setFlags(Intent.FLAG_ACTIVITY_NEW_TASK);
Rect rect = new Rect(640, 0, 1280, 752);
Intent e = mMWM.makeMultiWindowAppIntent(SMultiWindowManager.SPLIT_ZONE_B, null);
i.putExtras(e);
i.setDataAndType(Uri.fromFile(myPdfFile), "application/pdf");
startActivity(i);
}