Your question is not really clear on what is the problem, and what you want to accomplish.
I assume you're speaking about the HCM/HR module.
An employee that belongs to several companies will possess several employeeid's. If an employee occupies two positions in the same company, it will have only one employeeid (field pernr in all infotypes tables). However, it has two relationship with "S" objects (Job) in OM.
If you have an employee in several companies, you can create a solution. There are a lot of ways to do so (as always with SAP). It depends also on what (sub) module you want to use ? PA ? OM ?
In the first case, you could use a field of the IT0032 (badge for example), or create a shared infotype, with a GroupId / UniqId that is filled during infotype creation.
In the second case, you could use the "CP" object (central Person) in OM to get a relationship with all the P objects (person / employeeId) of the employee.
It really depends on the HR Processes and the current customization of your SAP system.