One PPCscope account can have multiple Amazon seller accounts, you can simply switch between them. We use MWS and their Advertising API, and each is connected in isolation. Each sub-account will almost “act on its own”.
During the PPCscope trial you can only add one Amazon account so you would need to subscribe to a plan to add more.
If you have further questions, please reach out through the blue button at the bottom right of this page.