One more explanation how to store contacts in EPESI.
Our philosophy is to keep things simple. Therefore a contact is a contact, company is a company. You can group them however you like but if you are looking for a name of a person it will be in CRM Contacts module. Your clients, vendors, suppliers, emergency phone number to the alarm company - and so on... all of it is treated the same way.
You can have a contact that does not belong to any company. You can have a company that has no contacts.
When you have a contact that belongs to a company - this is simple: just assign it under Company Name field.
In cases where a single contact can be associated somehow with more than one company - just assign the main company under Company Name field and then assign one or more companies in the multiselect field: Related Companies.
If you want to build a structure that reflects an organization with multiple branches - install CRM - optional module (free) called Parent Company.
In your case - enter the owner once with his e-mail address. Enter name of the first company as main company (Company Name field) and name of the second company under Related Company field - and this will do the trick.