You can later choose to enable it for your entire marketplace (Amazon or Ebay or Both) or only on select items.
Buy Box Owner subscription plans can be found by going to Settings --> Add Ons --> Buy Box Owner.
Here is a full playlist of tutorials on using Buy Box Owner - https://www.youtube.com/playlist?list=PL1P6jkYBkBWEI1zvXQMQ4huTtoJSPJDs3
If you're only wanting to use it on select items would be (after purchasing the BBO subscription) to go to your Amazon Marketplace Settings (Settings --> Marketplaces --> Amazon --> Country) and leave
|Use Buy Box Owner algorithm on all items|
Set to No.
Continue to configure the rest of the BBO settings to your liking.
Then edit the individual Amazon items that you want to enable Buy Box Owner own, and scroll down to the bottom and there is an option to Use Buy Box Owner Algorithm.
Set it to Yes on the individual items you want to use it on.
It would also be recommended to add a "Tag" to those items that says Buy Box Owner so that you can visually see which items you've enabled it on -- in case you ever want to turn it off, etc. Here's a video on how to use Tags - https://www.youtube.com/watch?v=fRUB51mwOCY
In doing it this way, you're not using Buy Box owner for any eBay items. You've configured it for Amazon, but you will only apply it to select items.