Hm, I did Jalup first and then came to WK, so my situation is a bit different, but I don’t see any specific problem with using both. (As long as you don’t overwhelm yourself).
Specifically, since they don’t show you things in the same order, you will primarily learn some word/kanji from one source before getting it in the other. That’s fine, repetition is important. Don’t skip the card if it’s in Jalup.
Other than that, you could check the ANKI template thread on this forum to help spice up the cards. There was also a thing called Jalup NEXT That was starting when I was done with Jalup, so I don’t remember too much but I might be better than doing the cards in ANKI as well.
(Also, you can check kitsun, also on this forum)