So first, I would recommend not getting too caught up in the idea of “organ” - “system” is much more appropriate word in Chinese Medicine terms. For the liver and kidney systems, I would recommend you start by reading “My liver is what?” and “My kidneys are what?” - which discuss the basics.
Specific to your question, how to you know what systems are involved - honestly this is what practitioners do. It takes many, many years to fully understand the diagnostic system of Chinese Medicine and even with a good understanding it is not a hard science. A practitioner will go through your entire medical history and look at your entire picture overall, not just what you coming in for, and use all of that information and more to come to a diagnostic decision. For the basics of that see “Treating the cause vs. the symptoms”.
For your second question, the kidney system is affects water balance in the body (among other things). When the system is weak - water can pool and/or not move well - so some places can be swollen (edema, for example) and other dry (constipation, for example). However, the kidney system can have yin deficiency (dryness) or yang deficiency (cold, wet) or mixtures of both. This is where the diagnostic process has to be looked at very deeply and broadly otherwise you are likely to come up with superficial diagnoses.