A few quick-and-easy answers, which I will say loudly (well, type loudly), because triathletes and endurance athletes are notoriously bad at this:
LISTEN TO YOUR BODY
REST & RECOVERY ARE VITAL PARTS OF YOUR TRAINING
YOU WILL NOT GET FITTER IF YOU DON'T REST & RECOVER
Study after study shows that exercise and sleep have a very important connection with each other: getting enough sleep plays a critical role in healthy adaptation from exercise, and getting regular exercise plays a critical role in getting a good night's sleep. So, each of us needs to find a good balance of those factors to stay healthy, especially now that the weather (in the UK, anyway) has taken a very autumnal turn, the hours of daylight are getting shorter and shorter, and it will be like this for another 6 months or so. At times like this, most endurance athletes pride themselves on their toughness, their resilience and, well, their endurance. Especially here in the UK, we are pretty good at enduring cold weather, rain, ice, mud and white vans. A few sniffles, a little cough, a minor fever or headache, a little twinge in the left calf, or some tightness in the shoulders isn't going to stay these athletes "from the completion of their appointed rounds" (with thanks and apologies to the General Post Office in New York City).
Half the time, that toughness is a great quality that makes most of the people I work with determined and diligent in their training, even when it is wet and cold and dark and miserable outside. And, the other half the time, that same toughness is not such a great quality that makes a lot of the people I work with a little too stubborn and prone to overtraining.
So, here is some good advice I have picked up and would like to pass along to you at this time of year:
If you have a cold that has moved into your throat or chest, take the day off, maybe a few days off, until you feel completely better.
If you got a really bad night's sleep and you wake up with your Resting Heart Rate elevated (assuming you know what your Resting Heart Rate is, under normal circumstances) by more than 10 bpm, take the morning off, maybe the whole day off, until you get back to normal.
If you have an injury or a persistent ache that just won't go away, take the day off, or a few days off, until you feel completely better.
Don't take short-cuts. For example, if you take a day off, get impatient, feel a little better than yesterday, but still not 100% better, then keep taking it easy and don't jump straight back into your normal routine until you feel completely better.
Training while injured is stupid.
Training while sick is stupid.
It is not tough or macho or proof of your super-human qualities. It is a waste of time that makes you weaker and less fit.
If you think you have the ability to "train through" or "train away" an injury or an illness, all that demonstrates is your extraordinary capacity for self-denial and the human body's amazing resilience in spite of your stubbornness and ignorance.
Sorry to be so blunt, but it really is that simple. As a coach, I have very little time for athletes who try to demonstrate macho, tough, super-human abilities to endure all manner of illness and injury without stopping. As an athlete, I know only too well what it feels like to be out of action for weeks and weeks, perhaps even months and months, because of my own failure to acknowledge and address a nascent injury or illness before it escalated further. It's stupidity of the worst, most self-serving, self-deluding, self-centred variety.
I know it is hard to tell when you are just feeling a little run-down or genuinely, full-on sick. It is hard to tell when you are feeling just a little niggle or genuinely injured. A good rule of thumb is that, if it didn't go away by itself within 48 hours, then you are probably leaning towards the side of genuinely sick or genuinely injured.
I also know, only too well, that sports training and physical activity is a hugely important part of many athletes' lives. I absolutely love the feeling of doing a good swim set, going for a beautiful run through the park, taking a zippy bike ride for a few hours, or punching and kicking the stuffings out of the heavy bag. These are things that have become very important to me, my sense of well-being, and my sense of who I am in the world. So, the idea of NOT doing one of these sessions in order to make myself feel better, is a hard one to grasp for me, and so it is for most dedicated athletes. Sometimes we can feel like "quitters" or "losers" or "wimps" when we take time off, and that is a mind-set I beg you to try and avoid.
Sometimes it is just a matter of dialing down a little in your training, reducing the hours of training, reducing the intensity, or doing something complementary (e.g. a yoga class, a pilates class) that takes the strain away from the overworked area. Obviously, if the overworked area is "your whole body", then you need to do something more than just dial down a little. Sorry, I know, it is hard to know what to do under these circumstances, and there are very few hard-and-fast rules here.
If you have a training plan, then ask yourself, "what is the goal of this next session?" (e.g. not "just to do some hard miles" but maybe more like "to develop muscular endurance while running uphill") and then ask, "can I accomplish that goal in this next session?" If you think that you are not in optimal health to accomplish the goal of that session, and you are already thinking about ways to cut corners, then drop it or change it. If you have a coach, discuss it with him or her and see what you can do, together. Sometimes you can also get good advice from a doctor, a nurse, a masseuse, a personal trainer, or some other trained professional. In the end, though, it comes down to you taking ownership of your health and well-being, recognizing the warning signs, and taking good care of yourself.