Confusion remembering the Kun and On'yomi Readings

I use the KunOn script. Of course, it doesn’t tell you which kun or on reading it wants when a kanji has multiple, but it still saves time when you know if it wants kun or on’yomi. But aside from that, you really will start to get a feel for it as you come across more words, both with which kun/on reading you use and with telling whether a reading is kun or on/what the difference between them is.