Learn both the main kunyomi and onyomi of each kanji that WK presents.
WK does not state it explicitly but all (well 95%) of 2-or-more-kanjis vocabs use the onyomi pronunciation.
For the single-kanji words, as well as words which contain some hiragana (verbs-adjectives) you will need to use the kunyomi pronunciation.
In the first levels, the kanji are mostly pictograms (drawings, like hieroglyphs). No trick, you need to learn them all, on- and kunyomi.
But in later levels the kanji are very frequently phono-semantic compounds. In such case, at least one radical gives an indication on the meaning, while an other radical gives a hint of its onyomi pronunciation (with variation, because pronunciation may have shifted when it was imported from China).
It will be much easier to learn the on pronunciation of the phono-semantic compounds, and thats great because this category represents 90% of the Japanese kanji.
There is no strategy for the kunyomi, you just need to learn the mnemonics ( that is mostly verbs and adjectives).