This is entirely up to you and depends on your resources. Although the independent configuration can help you when things go wrong or when they decide to hire someone else and you have to give them their DB and Files, maintaining a single codebase and DB saves so much time that can account for the costs of the other choice. In my own setup I have 3 separate installations. One for my company, one for commercial hosting and one for community hosting (free). I separated each in its own IIS pool and gave rules for bandwitdth.

All that being said, each business case is different so take some time to develop some guiding points for your own business It will take longer to take a decision but it will be better founded.