If there are a few rules of thumb that I've accumulated over the years, these are the ones I'd give to a younger me.
*Finding the things that count is what it's all about
When I first started squatting, a high-bar position was all I knew. I stuck with it for years. When I figured out how to hold the bar lower on my back, I instantly added a comfortable 50 pounds to my squat and then stuck with it for years. While sticking with those positions for years forced me to really work with them and learn them, I realize now that a single-minded drive for higher and higher loads in a single measure (unless you are a powerlifter) is misguided. When I start to get achey or a-holey, it's time kick back the load and try something new.
Don't misunderstand me here; I'm NOT saying that getting strong isn't important - I'm simply saying that "strong" isn't limited to what you can do on a single metric (be that an exercise or program) and that, in Albert Einstein's words "Not everything that counts can be measured. Not everything that can be measured counts." To make things more complicated, some things count sometimes, but not always... Finding the things that count is what it's all about.
*Frequent squatting makes it easier to gauge how you are feeling from one session to the next
I don't recommend people to squat daily, but when I was doing the "Squat To A Million Pounds" drive to raise money for Tsunami victims, I went a stretch of 70-something days, squatting over 10,000 pounds everyday. In retrospect, I should have done a better job of conditioning prior, but it was a sudden thing that I felt I needed to do.
The most enlightening parts of that experience were the daily feedback I would get from "yesterday's session", and figuring out how to include a thorough and proper warm-up every time even when under time constraints.
*Unilateral work is something to try to include in the mix
There are a lot of squat variants that most traditional squatters overlook. I like Bulgarian Split Squats, but there are other options. A single kettlebell front squat, for example, while not what most people think of when they think of "unilateral", is a great way to unevenly load the squat movement - I've been able to do them even with mild back strains when I could not do barbell squats. Lunges, while certainly not an exercise I'd recommend for everyone, are about as common as a squat below parallel with three wheels at the local fitness club. Turkish Get-Ups (most techniques anyway) include a lunge in its execution, so if you're struggling to get your unilateral fix, a good dose of TGUs can do the job.
*Switch things up before they mess you up
When I was a kid, we used to say "If you 'love it', why don't you marry it?". We'd say it dripping with heavy sarcasm and the thought of it still makes me laugh. Don't be married to any one squat variant or training program - it doesn't matter how much you 'love' it. As much as I love the idea of Smolov, Smolov has not been good to me. Beginning it, and then feeling compelled to continue until it's done, or I'm done, has left me broken more than once. In this post, Three Is a Magic Number, I talked about three weeks being about as long as the body will care to really, really push it. After that, even if you are still gaining (unless you are a beginner), it's probably going to be in your best interest to change things up. The change can come in load, volume, rest intervals, movement variation, training frequency, etc. - doesn't mean you have to throw out your current program, just that you be willing and able to change it when necessary.
*Stretching, mobility, working out the kinks - whatever you call it, do it
I've realized that I have a very different working definition of what "stretching" is than many other in the strength and conditioning, and fitness fields. That's fine - I don't like arguing about jargon, buzz-words, and phraseology. Most people can agree, I think, that moving well (mechanically sound and pain-free) is very important and that's what really matters.
In my opinion, stretching, mobility work, massage, electro-stim, ice, NSAIDs, compression, bands, roller, sticks, etc. are all tools for a job, and they all have their place in the recovery and movement prep arenas. Find what works. Experiment (safely and intelligently). Beware the hucksters that tell you that any of the above are horrible, because I've tried them all and they all work very well given the right conditions.
Squat-specifically, spend time working on your shoulder, thoracic, scapular, hip, hamstring, and ankle mobility and strength - if those are feeling good and strong, you're bound to squat more smoothly and with less issues.