|Although you report to the controller, it sounds like things are getting out of control. There is a rift between two corporate leaders, and you have become a corporate pinball.|
Your next step depends in part on some specifics in the company. In some companies, the owner plays a visionary and entrepreneurial role. When he or she gets involved in operations, people tend to respond with a wink and not much more. In other companies, an entrepreneur can be highly involved in day-to-day matters and play a key role in operations.
If you are in a company where the owner dabbles in operations without much of an impact, then your best step is to follow the directives of your manager, namely the controller. However, if the owner is more directly involved in operations, or if you are uncertain over his actual internal role, then it's time for a meeting of the minds. You should ask to meet with both of them, give them examples of the conflicting assignments, tell them you do not know whose directives to follow, and then ask for their help.
If either of these individuals has any operational skills, your message will be heard. The sooner they get their act together, the sooner you will know how to act.