@Saida touched on this, but I think one of the best ways is to tackle words like these as a phrase rather than a single word with several meanings.
For example:
(amount of time/money/resources)がかかる
電車で東京駅から自宅までは１時間がかかる
It takes one hour to get from Tokyo station to my place by train.
(something)に(something)がかかる
あの壁に、世界で1番大きい時計がかかっているよ
The world’s largest clock is hanging on that wall.
By doing this, each individual definition is conceptualized as an individual unit with an applicable format. I think this is explained better in this thread. It’s about making flashcards, but the idea is similar.
One more thing I’d add to this is tackle learning the each definition when you come across its application in a conversation or in writing rather than all at once.