Each girl has stamina (green bar) and arousal (pink bar), as well as a flower icon the represents purity. They also start each new game with a special 'virgin' icon. Virgin status makes them highly resistant to all forms of attack, and is very potent. However, their stamina will wear down as you use them, and once it's low enough, they will be knocked down and soon lose this bonus (which cannot be regained until new game+). Once this happens, it's a matter of keeping the pink bar low; each time it fills, the girl becomes more corrupted, until she is rendered too corrupt to participate in battle.
The key is to keep their initial stamina high and try to keep their virgin status. Using a character takes stamina, but the one (or two) that you don't use will recover it. This is why, if possible, it can make sense to take one girl with full stamina and leave the other two to recover, but this is only sometimes feasible.
The controls pretty much revolve around choosing which girls and which area to explore, but pay attention to how they are faring in combat. Special skills are costly in terms of stamina, but can help overturn a bad situation (for example, the floating monolith stones are very resistant to damage and can tear through even a healthy party, but can usually be dispatched by a single grenade special). If the going gets bad, escape and rest.
Losing and letting the game roll into new game+ gives a slight boost to maximum stamina, but it can take several, several rounds of this to see a noticeable difference. Keep in mind, though, that more stamina means the girls stay vigins for longer, which keeps them pure longer, which makes the game easier, so even a slight boost is helpful (if you;re having a hard time, though, it's not uncommon to have to attempt the game a LOT of times to get through the end). It's also worth noting that the final boss gets weaker for every area you clear before facing her.