I just sorted all of my cards (pilot and upgrad cards) into a binder and have two boxes (one for ships, one for tokens and misc.)

The binder is faction separate

alphabetical by ship

then by cost of ship lowest to highest

then epic at the end

and in the back its

Alphabetical by upgrade type with each upgrade type with its own section

then by cost lowest to highest

alphabetical in identical cost

and then the damage cards in no order but separated, I have three decks worth so I just pick the proper amount of each damage when I play and shuffle it,

Then Epic Upgrades organized similar to above

and then Epic Ship Damage with ship Titles at the top to differentiate the different damage decks

How about you guys?
How do you organize?

Ships are stored individually with standard tokens (1 focus, 1 stress, 1 TL if applicable, shields where available), base and baseplate and dial.

Pilot cards are separated by faction, by ship type, sorted by PS.

Upgrades are sorted by type.

Asteroids are stored with dice separate from all other tokens.