"Rest or regeneration is the most essential part of training for inducing optimal biological adaptations."-- Jan Olbrecht in "Science of Winning"
Growth factors (~GH, IGF-1, insulin) counter-balance the stress hormones (cortisol/glucagon/EP/NE) and stimulate tissue repair (~protein synthesis--> muscle, bone, etc.). The ability to get adequate tissue repair, and thus enhanced performance, is very much dependent on your sleep (~GH released), diet (~essential amino acids from complete protein sources), and balanced training (easy days easy).
These hormones also up/down regulate metabolic enzymes related to fat/CHO to provide fuel (ATP) for cells/brain (think pathways in glycolysis, citric acid cycle, fatty acid oxidation, glycogen synthesis/degradation, etc.). This depends on the type of training, with the outcome being more efficient metabolism. For example, with long slow distance running and double days (~glycogen stores half full), you down regulate glycogen phosphorylase (less glycogen breakdown) and up-regulate lipases (~hormone-sensitive lipase, muscle lipoprotein lipase) to enhance fatty acid oxidation-- thus the term "glycogen sparing". The utilization of fat vs. CHO depends on exercise intensity, oxygen consumption, and the respiratory quotient (CO2 expired/O2 consumed.... lower intensity = more O2 consumed = more fat metabolism). Intracellularly, changes in cAMP/etc. regulates gene transcription/translation of hormones, receptors, etc..
The term "use it or lose it" applies to both cardiac and skeletal muscle. Whether both "improve" at the same or different rates depends on the type/intensity of exercise and anatomical/physiological design (~fiber composition, heart size, gender). If you're working primarily aerobically, this will stimulate increased EPO production (more RBC production/hemoglobin= greater blood volume= more oxygen), increased capillarization around the muscle (~more blood and growth factors to muscle= enhanced recovery), and increased mitochondrial content (more aerobic metabolism = fat metabolism). If there's more blood and more capillarization, the stronger heart doesn't have to pump as fast or as hard to get blood, and oxygen, to the "working" muscle.
Overall, the neuromuscular changes sends a signal to the central nervous system, which in turn stimulates a whole cascade of hormones released, sympathetic stimulation of cardiovascular system, and increased/decreased metabolic pathways to provide fuel/ATP for cells (~liver, kidneys, muscle, brain!). The human body is very much integrated.
Hope I've answered your questions in a nutshell. This can get complex!:)