Regarding using binders for the negative storage...
(I am assuming that 'binder' means the same thing in US-English as it does in English - a stiff spine and covers, with several snap-close rings to hold pages in place).
Binders take up a lot of room and are not usually dustproof, but archival document filing boxes (acid free card, no glue, stainless metal fittings) can be filled with flat neg-pages, stored three deep on their long side and have plenty of space upon which to write references to their contents. Logical structure and a search-catalogue can best be arranged on a computer, or even with a card index if you don't trust electronic data. This packaging is far more protective of the contents, and more space efficient too.
For an unrestricted space and cost budget there are systems that are more protective, of course.