Once, a manga editor saw a note one of his creators had written that said "Grudge vs Ring was a cool movie", and he essentially said "go off on that". That's how we got DanDaDan.

A mangaka wanted to make a horror battle manga. Since there was already a lot of fighting manga, he decided to focus on competitive games instead. That's how we got Yu-Gi-Oh.

A mangaka wanted to make a death game series, but there was a gap in the market for casual romcoms instead. He then merged the two ideas together and had two tsunderes in mind games for romantic affection. That's how we got Kaguya-Sama.

There is no method to making good ideas. It's blind luck, flexibility and creativity, coupled with skill in executing whatever slapdash ideas you have.

See: Draw This, Then Die! (or the manga it is adapted from)

An unfortunately more realistic answer is "look for what's popular and copy that". For every hit there are dozens of low quality imitators.

They exercise their creativity. They produce a bunch of ideas and choose the one they like best.