yes there is. Invest in a tackle box for each faction, one for utobots and one for the decepticons. If you could find a good multilevel tackle box then that's better coz you can then stock up on more both smaller and large pieces.
My autobot Tackle box
my decepticon tackle box
a new extra organizer box I just bought from Reject Shop - it's smaller but has plenty or compartments which helps separate small guns and stuff especially if it's G1 accessories. There was a bigger one but I only needed this size.
I also use a tackle box for my other figures accessories - DCUC, MLs, etc. that way they are separate and I don't have to sift thru a pile if I only had it in a shoebox or some other non compartmentalized case.