NMM - Should be as simple as activating
Manual - Just extract the data folder into your Skyrim directory
That's it! SHR is now installed, and should be active as soon as you start the game.
No need for clean saves or anything like that.
Nothing fatal will happen if you just update the mod, by overwriting the new files, or let NMM do the job for you.
But I would suggest, that you save your game, with the mod turned off via the MCM before updating. I've had some minor issues in specific cases.
There shouldn't be any issue with just removing the files manually, or disabling with NMM. But it certainly wouldn't hurt to turn it off in the MCM beforehand.
Managing your heart rate
Your heart rate modifies your stamina regeneration. This is in both directions, so it is not simply a boost. A high heart rate will increase your stamina regeneration, while a low one will do the opposite. Increasing your heart rate comes quite naturally, whenever you do something of high physical effort. To lower your heart rate, simply relax. Sit down, stop running or stop fighting.
Managing your Long Term Stamina
Your long term stamina modifies your stamina. Again, this is in both directions, so a high amount will grant you some extra stamina, and vice versa. Furthermore, you will get a bit slower, when you reach very low amounts of LTS. LTS will decrease / increase depending on your heart rate. Keeping a high heart rate, will cause your LTS to decrease. Keeping an even higher heart rate, will cause it to decrease faster. To restore your LTS you will need to keep a low heart rate, and this is why it may actually be attractive to relax.
See Solving the Issue for detailed information