When you buy a mechanical seal from Yamaha, what you actually get is a 'seal kit'. This includes the rubber damper and its holder which sit inside the back of the impeller - which is I suspect what you are talking about? The oil seal (if you ordered one separately to the mechanical seal as well) would be an obvious single part.
It is not absolutely necessary to replace the damper and holder unless they are obviously worn. If you are going to do it, then you need to lever the olds ones out of the recess in the back of the impeller. (At this point, when you've got the old holder/damper out, how it all goes together.) Slide the new holder and rubber damper down the shaft and drift/press into the recess making sure they're flush. The two parts become one when they are pressed home. A good dousing in neat coolant makes everything slippery and much easier to get fit together.
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