Change Application folder presentation w/out disabling SIP I keep my apps organized in the /Application folder by arranging their icon manually.
But in El Capitan, SIP prevents the modification of this folder privileges so I cannot set it to read and write for my user and change the presentation options nor arrange icons manually.

I do not really want to disable SIP because of all bugs that seems to happen by doing it (even if I quite manage OS X since a while).

How can I manage to arrange my Apps icons without having to disable SIP?
Thanks
You don't. That's what System Integrity Protection is all about. But keep in mind you can disable it, do your changes and reenable it again. Both steps are described in How do I disable System Integrity Protection (SIP) AKA “rootless” on OS X 10.11, El Capitan?