Yes, it does get a lot easier, and a lot of this will start falling into place if you keep studying! I definitely experienced that myself.
I would recommend installing a couple userscripts that might help your understanding. The first is the Rendaku Information script, which adds a section to the lesson information for every vocab word and explains why it does and doesn’t rendaku. The second is the Keisei Semantic-Phonetic Composition script, which adds information about the composition of the kanji that can be really, really useful when trying to figure out the on’yomi reading for new kanji.
If you install the scripts, it’ll probably be a little overwhelming at first and you won’t know quite what to do with all of the information, but over time, you’ll start to notice patterns. Both of those scripts have really helped me understand the difference between on’yomi and kun’yomi readings and how rendaku works.
If you want to do a little deeper reading, Tofugu has an article on rendaku and an article on on’yomi and kun’yomi readings. If you’re like me, you will probably read these and quickly forget a lot of the information 
. But the good news is that WaniKani provides countless hours of practice for both, and even if you find this really confusing at first, the more exposure you get, the easier it will be to slot the information into place and make sense of it finally.