"organize differently" is correct and usable in written English.
You can use it when you want to express that something should be arranged in a different way, for example: "We need to organize our resources differently if we want to maximize efficiency."
While many components involved in these biological processes are identified, how components organize differently in health and disease remains unclear.
— Jenna Wortham Networked Norms Danah.org | A popular Web researcher on how tech start-ups and teenage practices organize differently.
The cells themselves develop normally — the programmed DNA isn't in the cells themselves, but rather is laid down in a sort of template that causes them to organize differently.
Nucleolar machineries organize differently when ribosome biogenesis is inhibited [ 43, 44].
The authors suggested that words of different form classes may be organized differently in learners' mental lexicon.
For example, tribal governments may be organized differently, tribal decisions may be made via differing formal and informal processes, and authority in various spheres (e.g., political, traditional, or cultural) may reside in different places (Cornell 1988; Williams 1994).
The sidewalk pansies show that Tokyo is organized differently than United States and European cities, and that many of these differences are nearly invisible to Japanese people.
Team sports are organized differently.
(Neither story was inaccurate, mind you, just organized differently).
The layer arrangement needs to be organized differently depending on the individual users.
Because mathematics testing in California's high school grades is organized differently than in English language arts, so too is the EAP in mathematics organized differently.
