Im wondering how to set FCP audio setting.

I can in Sequence setting set 48/24 but there nothing about the little or big endian.

Is FCP always in Big endian ?

As far as I'm aware, it is always Big Endian. The conversion from Big Endian to Little (and vice versa) is very inexpensive so the performance difference should be negligible.

My software:
Pro Maintenance Tools - Tools to keep Final Cut Studio, Final Cut Pro X, Avid Media Composer and Adobe Premiere Pro running smoothly and fix problems when they arise
Pro Media Tools - Edit QuickTime chapters and metadata, detect gamma shifts, edit markers, watch renders and more
More tools...