I don't think that there is any system that is perfect for everyone.
My millennium collection is stored as such [ subject matter].
My A/C chips are stored with LE's in order of release and house chips by casino.
Some others by geographical area and some just in racks.
While I haven't created a data base for my chips as many others have, that electronic system might be the best way since you can cross reference your collection many ways.
You can then just store them in some numerical order if you wish in boxes or trays.

Some of my collecting buddies keep much of their collection in chip racks simple because many of the albums can cause certain colors to bleed although I believe that can also happen in trays but perhaps to a lesser degree.
I trust that I have now confused you more