I write my own manga too! :D ... and... Well, i came up with some story lines while sleeping O_o ... And i think of some new ideas totaly randomly and i always write them down ASAP... So... i don't really think there is a "best way" to come up with a story, it just randomly comes... Also bạn could find a good idea just from your everyday :) (And bạn can change that into any genre bạn want)
I draw my own manga for fun so I am no professional at all; but bạn come up with a storyline just as bạn would with a book hoặc any other story. As manga is often serialized, however, it's best to have a storyline that can span for quite some time without the reader getting bored. Sub-plots are essential.