I haven't tried deploying a Polylith project to Ions yet (although I will be next week and can let you know how it goes) but based on some somewhat related experiences I can give you a few tips:
You would still need to use Leiningen for the Polylith tool as they are heavily integrated together. You would also need to make sure that the commands
lein compile and
lein test work in each of your components/bases, and possibly that
lein uberjar works in your systems if you want that (if not, you can edit
build.sh in the system folder to change /remove that step).
In other words, you need fully functioning project.clj files for each piece of the project, and ideally you would manage your dependencies in those project.clj files as well because then Polylith will keep them all in sync for you automatically and take out a lot of the effort.
What I'd suggest would be to embrace using leiningen to manage your polylith project, and then use something like depify to create a deps.edn file programmatically for your Ions deployment. The place you would want to do this is inside the directory of the system that you want to deploy to ions, and I think a good place to do it would be in the build.sh script ?
Alternatively, you can still use the polylith concepts without the polylith tool, but frankly the tool makes it a lot better! And imho Leiningen is pretty nice, having used tools-deps for a while on a few projects I've ended up going back to Leiningen on all of them as it's simply a much more mature and fully featured tool.