There are two ways of managing Amazon variational products:
1. Import items as Unmanaged Listings and link them with Magento items
Variational Product on Amazon provides ASINs for a Parent product as well as for each Child product. However, only Child Products can be imported as Unmanaged items via Amazon API. Parent Products will not be imported.
You can map each Child product to existing Simple products in Magento, move them to an M2E Pro listing, and continue managing each Child product separately under existing ASINs. This way your product will be presented on Amazon as Variational, only M2E Pro will manage its variations as separate Simple products.
After you move a product from an Unmanaged Listings to an M2E Pro listing, it needs to be Revised so that the connection between mapped Channel Item and Magento Product it was mapped to.
2. Link Magento and Amazon Variational Products by SKU
Create a Variational product in Magento identical to the one you have on Amazon (same SKUs, titles), add it to an M2E Pro listing, and list it under existing ASIN (the same you have on the channel) using this instruction. After this M2E Pro will automatically find an item with the same SKU in your Amazon Inventory and link it to this Magento Variational product (Parent and Child products). If the linking is successful you will see a log "Product has been found by SKU "***" in your Inventory and successfully linked".