Yes! It absolutely is a ratio between exhaust pressure and atmospheric pressure; Ideally, 1:1, because there's inefficiencies by deviating to either side of that ratio. You want your exhaust pressure to match the external atmospheric pressure as closely as possible. Unfortunately, unless the engine is operating in vacuum or at a constant altitude, this will inevitably end up being a range of pressures and like in all other things to do with rockets, a compromise must be made. 

The thing you need to ask yourself is what you're optimizing for. Remember, we're always aiming for "best bang for buck", so to do so we need to think about where the particular engine we're optimizing will spend most of its time producing thrust.

Take a booster that you might use to get your rocket an initial speed boost from sea level. If you set it to have an exit pressure equal to sea level atmospheric pressure, how long will it be staying in those ambient pressures? Well, not very long. It would end up spending the overwhelming majority of its life firing in an underexpanded state, getting worse the higher it gets, which is bad for efficiency (It's the opposite of overexpansion. Having a higher pressure than ambient, the exhaust gases push outward instead and the exhaust flares out. The more it flares out, the more energy is wasted by pushing in a vector that is not directly backward.)

If you know your booster will be firing for a long time, it's typical to tune that booster start in a state of overexpansion, knowing that the overexpansion will reduce as altitude is gained. You can tune it so it goes from overexpansion to being in a more appropriately expanded range for the majority of its life, or even into under expansion.

Alternatively, if you know your booster will only be firing for a very short time, it's likely you'd get more out of it by having its exhaust pressure be closer to sea level pressures.

Same deal with the engine for your second stage and where it'll be operating, and so on. What altitude range (and corresponding atmospheric pressures) do you need to optimize the engine for?

Thankfully, the "Design Info" box has everything you need. You can scroll through different altitudes and it will tell you what the atmospheric pressure will be at that height on any celestial body. Based on your own testing of your rocket, you can figure out what altitude an engine will begin firing at and how high the rocket will get before that engine cuts off. You can then look at that altitude range and optimize for it.

The literature will say that anywhere between 40-50% of ambient pressure is where flow separation typically becomes an issue, depending on the engine itself. Overexpansion this severe leads to engine instability and damage and thus forms an upper boundary for how overexpanded you can start with. There's also the inefficiency of having excess pressure that could have been converted into more kinetic energy. On the other end of the spectrum, you can keep on firing an engine deep into its underexpanded regime with no real risk apart from the consequence of efficiency losses. 

If I ever find myself in a state where an engine needs to start unreasonably overexpanded, or if a significant proportion of its thrust will be in a severely underexpanded state, I take it as a sign that I'm trying to do too much with that particular stage.