The grammar orderings for textbooks and other resources are actually secondary to the ‘default’, built-in BunPro ordering. Because of this, by following one of these secondary orderings right off the bat, I think I can understand why it might be seeming disconnected and difficult. But first, let me say something about the default, built-in BunPro ordering:
While the BunPro ordering for grammar points ostensibly is ordered just by the JLPT levels (starting from the easiest N5 to the most difficult N1), the BunPro ordering is much more intricate than that ‘rough’ ordering. The grammar points are generally, more-or-less ordered in such a way that they build upon previous grammar points – well, the first few grammar points are stand-alone, though.
So, if one were to follow the BunPro order – e.g. by going to Settings > General > New Grammar > JLPT Study Level, and selecting “JLPT5”, and then using the Study button or clicking on “New JLPT5 Grammar” on the dashboard page – one would start with the simplest grammar points, だ, です, は, も, etc. The complete BunPro ordering of all of the grammar points can be explored under Content > Lessons (BunPro Grammar Order) at the top of the dashboard.
In this way, BunPro tries to make every lesson build upon previous lessons.
But, if a particular textbook uses an order that starts off with grammar points from somewhere in the middle of BunPro’s ordering, then (for example), some of the example sentences will use grammar points you’ve never seen before.
Even more striking is that, especially later on, you will be expected to do things like conjugating verbs within your answer, using conjugations that you may not have learned yet, if you’ve jumped ahead too far out of the BunPro ordering. So, not only will you be trying to read sentences with grammar you don’t know yet, but you also might be trying to answer an answer that requires you to use grammar you haven’t learned yet.
So, I suspect this is probably the main source of the ‘disconnection’ you’re feeling.
Now, in an ideal world, BunPro might somehow be able to accommodate all of the various textbook orderings perfectly, so that it never uses any grammar you haven’t already covered. Unfortunately, we don’t live in that ideal world, and the only thing that using a textbook’s ordering does at this point is to simply provide the BunPro grammar points in the same order that those same grammar points are covered in the textbook – but at the cost of being in a ‘mixed up’ order with respect to the default BunPro order.
So, I have two main suggestions, and a follow-up suggestion:
- Start yourself off in BunPro, for at least a few lessons, by following the default BunPro ordering – and then later switch to your chosen textbook’s ordering, once you’ve got the BunPro basics under your belt. This will at least give you a kind of ‘foundation’ of grammar points you’ve learned to get a better feeling of how things are ‘connected’ in BunPro . When you start following your textbook’s ordering, things ought to flow more smoothly and be more ‘connected’.
- Alternatively, if you’d prefer to strictly follow your textbook’s ordering, then I’d suggest trying to follow your textbook’s lead more closely, and only think of BunPro as a mere ‘tool’ which is assisting you by at least providing a system for you to start practicing your textbook’s lessons in addition to what exercises the textbook already provides. In other words, if you find grammar in BunPro you haven’t seen before, just think to yourself, “Ah, that’s just a quirk of BunPro. I don’t need to worry about that stuff yet. I’ll just stay focused on the specific lesson my textbook is trying to teach.”
[Note: In truth, with BunPro you can technically do the grammar points in any ordering you want. In particular, if there’s a grammar point that’s causing you confusion because you haven’t learned it yet, you can look up that grammar point using the Content > Grammar (All BunPro Grammar & Search) menu option, and add it to your reviews. That way, at least you’ll be able to answer the textbook’s grammar points again.]
Followup suggestion:
By all means, if it is painful or troubling to use BunPro for any reason, I do recommend submitting feedback, either on the Feedback - Suggested Improvements/Feature Request and Feedback - Bug Reports threads, or via the various reporting features, such as the Report button or the Ask a Question button at the bottom of grammar point pages, or the +Report button on each review sentence (after answering).
The BunPro team are quite good about responding to feedback and bug reports. They may not be able to solve all problems immediately, but they will at least read and listen and make plans to improve your overall experience of using the site over time. For example, if you discover that you’ve come up with a suggestion to improve how BunPro could work better for people who start off by using a textbook ordering, I’m sure they’d love to get some feedback about that so they can improve BunPro for those folks.
Anyway, hope this helps a bit. Good luck! Oh, and just keep at it. I also found learning grammar frustrating and ‘disconnected’ at the beginning, and for the first while. But over time, keeping practicing, things start to make more and more sense, you also start to get a better feel of how BunPro works and how to make it work for you better, and the frustration will (eventually! 
) fade away!
