Civilization Beyond Earth allows your soldier units to be upgraded to better commandeer through the alien planet you’ve inhabited. It’s very simple to upgrade them, so don’t fret.
All you need to do is increase your civilization’s affinity with harmony, purity, and supremacy to unlock upgrade tiers for your units. You’ll be brought to a menu when an upgrade is available, as it becomes part of your to-do list, so to speak. So yes, the game itself will let you know when an upgrade is available. You start with level one and can go all the way to the maximum level of affinity for each of your units.
Each upgrade level allows you to choose from one of two perks. At first, you’ll have to increase your affinity once, but then you’re going to have to zero in and focus on which affinity you want to level up. In order to have all three max upgrades for each affinity, it will take you 33 levels in total, for example. So, past level one, your affinity level starts to matter and you won’t be able to use purity levels with harmony’s upgrades. However, after hitting 10 with one affinity, you’ll have the opportunity to mix and match affinity levels. For example, you might have 10 purity and 4 supremacy in order to get a certain upgrade for one of your units. So, the game definitely rewards those who branch out.
In case you want to see your units available upgrades and keep track of everyone’s progress, hit the triangle looking icon on the bottom right (hovering over it reveals it is the Upgrade Units screen). This is useful for bigger picture planning for your army.
Oh, and different perks and upgrades change your units’ appearances. Pretty cool, right?