The Master SKU is the SKU that LM uses to keep track of a listing.
The Marketplace SKU is the SKU that exists on the marketplace.
These do NOT have to be the same. If they are not, the marketplace SKU will show up as the alternative SKU under the Master SKU on the Manage Listings page. See image.
In the above image, the SKU on Amazon is 12343 and it is blue-scarf-hat-gloves-set on eBay. The Master SKU is bluewinterbundle. LM knows all of these listings are the same on, spread out across the different channels.
This difference will not matter to Listing Mirror. Even when you receive an order from a marketplace, where the SKU on the marketplace does not match the Master SKU, LM will still know which item it is. In the Order Details page, you will see both SKUs listed.