+1 for what Wyno said.
In my LowePro 28lt pack I use a generic soft camera bag insert similar to this which fits around my 4x5 perfectly (take out the middle insert of course):
and then I have a few zip up cushioned protective cells like this (one holds my double darks, another the misc items like loupe, meter, level etc.)
My dark hood, and other miscellaneous items have there place in the pack (water is via a camelback, food and other field tools/safety items go into the various pockets in the pack itself or on the shoulder webbing).
My tripod then attaches to the back of the pack with webbing.