I have been using Bunpro, but I don’t really get what it says about the differences between は vs. が and で vs. に. How do you guys remember/think of the difference?
Allow me to introduce you to Tofugu, a wonky Japanese language and culture blog with detailed articles about both of those topics.
For my personal answer: I don’t worry about them at all. If you do enough immersion you’ll eventually reach the point where one just sounds right - the same way you know whether to use “a” or “the” in English.
は vs が is a too big topic to actually get into. The short story is that は marks topic and が marks subject. There have been whole books written about this and it can get very tricky. Just be careful because は and が can also be used for other things (e.g. contrastive は, possesive が, etc…).
で and に are completely different, and the distinction shouldn’t be that hard. They have various uses so if you tell us in which way they confuse you we can maybe narrow it down more. I suspect you mean the で marking a place and the に marking a direction if you are confusing them, but that is just an educated guess.
Since the Bunpro explanations don’t seem to work for you, I would recommend you look into other resources that explain grammar. Free online resources like tae kims guide (particles) or imabi (が は) might help you understand the topics better and are pretty well liked afaik.
EDIT: or the tofugu articles link before 
To add to this, I still get に and で mixed up, but I felt a lot better about it when I saw a Japanese instructor on YouTube explain it by saying they still don’t understand why English speakers say “going to the store” instead of “going at the store”. So, it’s just something you need to learn by reading more Japanese and seeing how they’re used. I don’t think に and で are interchangeable like that, but as a beginner, it can be hard to figure out which one to use sometimes.
That’s the way I think of them. I think of に as a destination marker and で as a location marker, but I still get them mixed up, especially when they’re not talking about a literal place someone is traveling to or existing at.
I have to agree with OP that BunPro’s grammar lessons are extremely confusing. I tried it for a month or two, but it all felt so abstract. Then I’d read a Tofugu article on the same grammar point, and it would be so much easier to understand.
Now, I’m no master of Japanese grammar or anything, but I think you’re better off just reading things you’re interested in and searching Tofugu articles for grammar points you don’t understand. Use a pop-up browser dictionary like Yomitan, if possible, because it’ll highlight grammar points when you look up a word, which saves you the trouble of having to figure out what you’re supposed to google when you don’t even know what you’re trying to learn about.
80/20 Japanese does a great job of discussing these distinctions, and particles in general.
Oh, cool! I’ve seen Tofugu before but didn’t notice they had an article on that, thank you! They explained it so well.
Thanks! What would you recommend to replace with Bunpro? I am having trouble finding a source to learn grammar. Looking up stuff I don’t know is good, but I’d also like a spot to learn new things and then encounter them later (if that makes sense).
ありがとうございます！
That’s the part I’m still trying to figure out. I’ve watched TokiniAndy’s Genki videos before, and the 80/20 Japanese is a great intro to particles, but I haven’t found much else.
There’s an Anki flashcard deck called JLab’s beginner course that I’d recommend. It’s mainly used for listening comprehension, but it’s based on Tae Kim’s grammar guide. I haven’t read through that guide before, but from the JLab flashcard deck, it seems to be more intuitive than Genki or BunPro. However, it does oversimplify things at the start. Still, I prefer it over the other two since I’d rather have an oversimplified understanding I can learn from than no understanding at all. (Also, I’d recommend learning Anki’s hotkeys so you can use it without looking at the screen. It helps when you don’t give yourself the chance to see the words on the screen).