Arduino automatically creates prototypes for each function but it does not handle user defined arguments (such as your structures) which is why your code wont compile. You can fix that by adding the prototypes yourself, just after the struct definitions – here is a fragment that has prototypes for the functions that take your structures:
struct Thermistor
{
int base; // *100, see below
int diff; // *10 because of floats (10.2, for example->102)
int pin;
};
struct Controller
{
int relayPin;
int thermInvert; // 0 = power on cools, 1 = power on heats
int lastRead;
int low;
int high;
int status; // 0=off;1=on
int toggle; // 0=nochange; 1=turnedon; 2=turnedoff; 3=malfunction
int timer; // seconds since last status change
struct Thermistor Therm; // Thermistor
};
// add the prototypes here:
void checkTemp(struct Controller &c);
void toggle(struct Controller &c);
void tooHot(struct Controller &c);
void tooCold(struct Controller &c);
void doOutput(char name[4], struct Controller &c);