How can I avoid flight simulator software reinforcing bad habits?

The best recommendation I can give you is to get a VR headset. Yes, they're a bit pricey, but not bad at all compared to actual flight hours in a real airplane. Practicing for visual flight just isn't very good with normal monitors.

Personally, I had been playing around with flight sim games for years before I ever flew a real airplane. I do agree that, if done only with normal monitors, it can train you to rely too much on the instruments. For the first maybe 2 flights that I performed in a real airplane, my CFI complained that I was spending too much time looking down at the artificial horizon on the attitude indicator, rather than looking at the actual horizon out the window. That said, after a couple of flights in the real thing, that problem was solved, so it really wasn't that big of a deal. Already being familiar with how the flight controls and instruments work vastly outweighed the need to 'unlearn' that habit.

Unfortunately, my primary training in the real airplane had some large gaps in it. Not long after my first solo, I had a gap of about 2 years between flights, due primarily to grad school, for example. Before I started flying again, I tried using the flight sim to get back in practice. However, even with yoke, pedals, throttle, trim wheel, etc., it was difficult to practice the sorts of visual flying that you do in primary flight training. I had a 3-monitor setup, but it still wasn't enough to be able to, for example, look over my left shoulder at the runway when flying a pattern. Yes, you can pan the view around, but it's not really the same.

Fortunately, shortly after that time, VR headsets came on the market. I purchased one along with an FSX add-on that integrates the headset with FSX. For visual flying, the difference is enormous. Aside from the lack of actually feeling the forces, things like flying a traffic pattern and just general visual flying are very near the real thing, especially if you can get a good model of the airplane that you're actually going to be flying. Just being able to turn your head to the left and see the runway out the window while flying a pattern is incredibly helpful, for example. The same is true for practicing other visual maneuvers, such as turns around a point. And, of course, if you have a good model, the inside of the airplane looks almost exactly like it does in real life. It's much, much more realistic than trying to pan the view around on static monitors.

Additionally, I'd recommend downloading a good terrain scenery pack for the area where you'll be flying. Rather than having the stock FSX terrain that just uses generic textures to represent forested land, small cities, fields, etc., a good, high-resolution scenery pack looks very much like the real thing, especially when combined with a VR headset. I was able to download one for my entire U.S. state (which, for comparison, is about 3 times the size of Switzerland) for a pretty small price. When they say this is high-resolution, they're not joking. Not only can I see my house, I can see individual trees in my yard. It's that good. This is very helpful for practicing visual flight, since you can see the actual landmarks that you'd using for visual navigation in real life.