It’s up to you how you do it as long as you have a unique copy of both the theme and the plugins for each individual site.
Bear in mind - if you buy a theme with plugins bundled then:
- You are only allowed to use that copy of the plugins with that theme (not any one you want)
- there’s a good chance the plugin will be customised to the theme so may not function correctly with another theme anyhow
- Bundled plugins do not give you the ability to auto update and you will need to wait each time there is an update for the author to release the newer version (assuming they do not stop updating the theme at some point in the future).
If it’s client work then my advice would not be to cut corners on it and actually get the client to buy the individual licenses for all themes and plugins required - that way they have access to updates etc. in the future should you part ways, and they can download any updates immediately without waiting for a theme author.