Hi,
Normally, GCC would handle the system include directories automatically, so VisualGDB does not offer any special settings for overriding this.
You could try adding the -nostdinc option to CFLAGS and then entering all include directories (system and regular) in the order you are trying to use, however we would advise against this, as such setup would be very fragile and could stop working if the internal directory structure of the toolchain changes in the next GCC version.