David,

First, I highly recommend that you pick up the book, EMyth Revisited. This is the best place to get a solid foundation of what you're wanting to do.

Functionally, if you have employees that span over one or more companies that you operate, the best solution is to build individual org charts for each company based on what it would look like if you had individual employees first. Then once the org chart is created, then you apply the names of people to the roles that they are filling in each company. What this will likely look like is one name on several org charts and potentially in several different roles.

The goal to this strategy is that you have an outline of what your company will look like when you're at 10MM, and you fill the positions with the people you have at 1.1MM. This will map out your staffing strategy when you grow, but also give your employees a full view and understanding of their role and place in each company.

I hope that helps.
Kyle