What you need is a way of tracking other's work for merit:
- Set goals with each person, those goals must align with what the company's goals are. Bonus, if everybody's goals don't fill all of the corporate goals, it means you need to think about hiring. If you have over representation in some goals, it means you're overstaffed in that area and need to work on moving people and developing them to fill in gaps.
- At six months see how they're doing in meeting those goals.
- At 12 months, do a full review.
- Set up a sliding pay-raise system.
--If they meet all their goals, they get some agreed upon number.
--If they miss a few, they get less.
-- If they miss half (or whatever you specify), they get nothing and an improvement plan that's checked on after 30-60 and 90 days with the normal six month review deciding if they can stay.
-- If they miss more than half, time to think about parting ways.
-- If they exceed their goals, give them a bonus (not an extra pay raise since those can live forever) and then think about giving them tougher goals next time.
As for work structure, you must have a hierarchy, otherwise one will develop naturally and it most likely won't be aligned with the needs of the business. This is what humans do in groups of 2 or more, there's no getting around it. Just take a person with some leadership skills and put them in charge of managing a group of related tasks, and reporting up how things are going not going. That extra responsibility also needs to be rewarded.
One options, make people task managers instead of people managers. They own the task and when its done, they move on to other work or get another task to manage. This can help you maintain the feeling of "flatness" while creating opportunities for different individuals to get experience being in charge of things.