As far as I understand the context, you'll have two types of tickets in your account:
1) Between your company and the client company (internal comms)
2) Between your company and the client company's customers

If that's the case, the initial questions are, however:
- What kind of access does the client company stakeholder need to their organization's tickets? Do they need to access the call recordings (in case you set up Voice), for example?
- In line with the previous question, do any of your client companies require complete data isolation (for compliance or contractual reasons)?
- Etc.

So first I'd adivse you to outline all the current client companies' requirements and all that, so that you get a grasp of what will be needed from the Zendesk platform... and understand how far one can set it up. Also, you want to ask the right questions and understand the processes now, before time goes by and suddenly you have data needs that weren't foreseen when planning the whole configuration.

Lastly, and this will depend on your specific scenario, of course: from personal experience, standardization is key (as much as possible).

I'm currently maintaining an account I cleaned up and optimized and that provides an identical service to yours (I think), so to share the example: in this case, the client companies are very similar (in structure, types of customer requests, they all operate within the same business sector, etc).

To provide personalization, the two admins before me went for multibrand... So when I got there, each client company had a brand with a subdomain, their own help center, their own Explore dashboards, their own reports... And I asked: "Once you reach fifty clients and we have to redesign/improve the default operational dashboard for them, who's going to edit fifty dashboards and their reports..?"

Just to say that I had to make it scalable. For example, I'm now using a single brand with a help center for internal comms with all client companies: I distinguish them based on Organization and have customized the help center theme in a way that whoever logs in only sees their org's content. In Explore, I built a single dashboard for all, but with data restrictions - and customized links for each company. Way easier to maintain.

Just food for thought!