Welcome! Make sure you come join in on the forum regularly! 
Answering your questions in sequence:
If the mnemonics arenât helping you, take a few extra minutes during your lessons and/or reviews to come up with your own that help you more. You can add them directly into WK.
If the remembering hiragana is an issue then it sounds like you need to take some time to review it. Try writing or typing them out in kana table order from memory. Once youâve done as many as you can make notes of ones you got wrong or ones you missed. Kana is the lynchpin here of going on to learn kanji and vocabulary so you need a strong base there.
Now as to knowing whether something on WK wants onâyomi or kunâyomi:
- Vocabulary with a single kanji or kanji and hiragana = usually kunâyomi.
- Single kanji (not vocabulary) or vocabulary with multiple kanji = usually kunâyomi.
In the wild? Pretty similar, I would say, but donât worry about this at this stage.
I say usually though because exceptions are always going to exist.
Check this link for more information about onâyomi and kunâyomi.
This a mixture of allowing the SRS to do its job and paying attention during your lessons.
Here are some things I like to do when I come across tricky kanji.
- Use this script to keep track of my leeches. If they become actual problems for me I handwrite them for later review. You could do that or you could review them on Anki or similar. Donât review them before a WK review though or youâll not benefit from the SRS.
- I also like to look up the etymology of kanji using this website. Sometimes itâs useless but other times it helps me create my own mnemonic and/or gives me a deeper understanding of a particular kanji.
Youâll come across ăă a few times. My understanding of it is that ăă on a ăăŒadjective makes it into a noun.
All I can say to learn the difference between 性ăă and 性ăă is experience, practise, and, maybe, additional work on it.
Finally, good luck with your studies!