I think you need something to distract ds whilst you are putting baby down for naps.
Is there anything he sits down for?
a favourite tv program or DVD that can be specifically for baby's nap time. And only on as long as baby is asleep and he doesn't disturb her.
Or go the other way and get him involved. Eg can you find dds a nappy, can you read her a book etc
6 is old enough to understand (Unless SNs) so would assume that this behaviour is deliberate.